Medical Genetics and Epigenetics - Ch. 1 - 4

What are some epigenetic mechanisms? How are epigenetic mechanisms different than genetic mechanisms?

3-8). Complex epigenetic states can be established, maintained, and transmitted by a variety of mechanisms: modifications to the DNA, such as DNA methylation; numerous histone modifications that alter chromatin packaging or access; and substitution of specialized histone variants that mark chromatin associated with particular sequences or regions in the genome. These chromatin changes can be highly dynamic and transient, capable of responding rapidly and sensitively to changing needs in the cell, or they can be long lasting, capable of being transmitted through multiple cell divisions or even to subsequent generations. In either instance, the key concept is that epigenetic mechanisms do not alter the underlying DNA sequence, and this distinguishes them from genetic mechanisms, which are sequence based. Together, the epigenetic marks and the DNA sequence make up the set of signals that guide the genome to express its genes at the right time, in the right place, and in the right amounts. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 33). Elsevier Health Sciences. Kindle Edition.

What is the function of the 5' cap and the 3' poly-A tail in a primary RNA transcript? Where do post-transcriptional modifications (i.e. 5' cap, 3' tail, and RNA splicing) take place?

A 7-methylguanosine cap is added to the 5′ end of the pre-mRNA while elongation is still in progress. The 5′ cap protects the nascent mRNA from degradation and assists in ribosome binding during translation. A poly (A) tail is added to the 3′ end of the pre-mRNA once elongation is complete. The poly (A) tail protects the mRNA from degradation, aids in the export of the mature mRNA to the cytoplasm, and is involved in binding proteins involved in initiating translation. transcript. All of these post-transcriptional modifications take place in the nucleus, as does the process of RNA splicing. The fully processed RNA, now called mRNA, is then transported to the cytoplasm, where translation takes place (see Fig. 3-5). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 28). Elsevier Health Sciences. Kindle Edition.

What are insertion-deletion polymorphisms aka indels?

A second class of polymorphism is the result of variations caused by insertion or deletion (in/ dels or simply indels) of anywhere from a single base pair up to approximately 1000 bp, although larger indels have been documented as well. Over a million indels have been described, numbering in the hundreds of thousands in any one individual's genome. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 46). Elsevier Health Sciences. Kindle Edition.

What is a gene map? A gene locus?

Each species has a characteristic chromosome complement (karyotype) in terms of the number, morphology, and content of the chromosomes that make up its genome. The genes are in linear order along the chromosomes, each gene having a precise position or locus. A gene map is the map of the genomic location of the genes and is characteristic of each species and the individuals within a species. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 3-4). Elsevier Health Sciences. Kindle Edition.

When does extensive demethylation generally occur?

Extensive demethylation occurs during germ cell development and in the early stages of embryonic development, consistent with the need to "re-set" the chromatin environment and restore totipotency or pluripotency of the zygote and of various stem cell populations. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 33-34). Elsevier Health Sciences. Kindle Edition.

How can histones be modified? What are the purpose of histones?

Histones can also be modified by chemical changes, and these modifications can change the properties of nucleosomes that contain them. As discussed further in Chapter 3, the pattern of major and specialized histone types and their modifications can vary from cell type to cell type and is thought to specify how DNA is packaged and how accessible it is to regulatory molecules that determine gene expression or other genome functions. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 8). Elsevier Health Sciences. Kindle Edition.

What features characterize a gene family?

Many genes belong to gene families, which share closely related DNA sequences and encode polypeptides with closely related amino acid sequences. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 25). Elsevier Health Sciences. Kindle Edition.

What happens during meiosis II?

Meiosis II is similar to an ordinary mitosis, except that the chromosome number is 23 instead of 46; the chromatids of each of the 23 chromosomes separate, and one chromatid of each chromosome passes to each daughter cell (see Fig. 2-14). However, as mentioned earlier, because of crossing over in meiosis I, the chromosomes of the resulting gametes are not identical (see Fig. 2-15). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 18). Elsevier Health Sciences. Kindle Edition.

Why does studying polymorphisms provide key elements for the study of human and medical genetics?

One might expect that deleterious mutations that cause rare monogenic diseases are likely to be too rare to achieve the frequency necessary to be considered a polymorphism. Although it is true that the alleles responsible for most clearly inherited clinical conditions are rare, some alleles that have a profound effect on health— such as alleles of genes encoding enzymes that metabolize drugs (for example, sensitivity to abacavir in some individuals infected with human immunodeficiency virus [HIV]) (Case 1), or the sickle cell mutation in African and African American populations (see Chapter 11) (Case 42)— are relatively common. Nonetheless, these are exceptions, and, as more and more genetic variation is discovered and catalogued, it is clear that the vast majority of variants in the genome, whether common or rare, reflect differences in DNA sequence that have no known significance to health. Polymorphisms are key elements for the study of human and medical genetics. The ability to distinguish different inherited forms of a gene or different segments of the genome provides critical tools for a wide array of applications, both in research and in clinical practice. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 45). Elsevier Health Sciences. Kindle Edition.

What are single-gene defects? How common are single-gene defects?

Single-gene defects are caused by pathogenic mutations in individual genes. The mutation may be present on both chromosomes of a pair (one of paternal origin and one of maternal origin) or on only one chromosome of a pair (matched with a normal copy of that gene on the other copy of that chromosome). Single-gene defects often cause diseases that follow one of the classic inheritance patterns in families (autosomal recessive, autosomal dominant, or X-linked). In a few cases, the mutation is in the mitochondrial rather than in the nuclear genome. In any case, the cause is a critical error in the genetic information carried by a single gene. Single-gene disorders such as cystic fibrosis (Case 12), sickle cell anemia (Case 42), and Marfan syndrome (Case 30) usually exhibit obvious and characteristic pedigree patterns. Most such defects are rare, with a frequency that may be as high as 1 in 500 to 1000 individuals but is usually much less. Although individually rare, single-gene disorders as a group are responsible for a significant proportion of disease and death. Overall, the incidence of serious single-gene disorders in the pediatric population has been estimated to be approximately 1 per 300 liveborn infants; over an entire lifetime, the prevalence of single-gene disorders is 1 in 50. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 2). Elsevier Health Sciences. Kindle Edition.

What is monoallelic gene expression? What are some examples?

Some genes, however, show a much more complete form of allelic imbalance, resulting in monoallelic gene expression - only one allele is expressed. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 37). Elsevier Health Sciences. Kindle Edition.

What direction is a primary RNA transcript synthesized? Where are the start and stop sequences generally located? Where is the promotor region generally found?

The adjacent nucleotide sequences provide the molecular "start" and "stop" signals for the synthesis of mRNA transcribed from the gene. Because the primary RNA transcript is synthesized in a 5′ to 3′ direction, the transcriptional start is referred to as the 5′ end of the transcribed portion of a gene (see Fig. 3-4). By convention, the genomic DNA that precedes the transcriptional start site in the 5′ direction is referred to as the "upstream" sequence, whereas DNA sequence located in the 3′ direction past the end of a gene is referred to as the "downstream" sequence. At the 5′ end of each gene lies a promoter region that includes sequences responsible for the proper initiation of transcription. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 25). Elsevier Health Sciences. Kindle Edition.

What is the medical relevance of mitosis and meiosis?

The biological significance of mitosis and meiosis lies in ensuring the constancy of chromosome number— and thus the integrity of the genome— from one cell to its progeny and from one generation to the next. The medical relevance of these processes lies in errors of one or the other mechanism of cell division, leading to the formation of an individual or of a cell lineage with an abnormal number of chromosomes and thus an abnormal dosage of genomic material. As we see in detail in Chapter 5, meiotic nondisjunction, particularly in oogenesis, is the most common mutational mechanism in our species, responsible for chromosomally abnormal fetuses in at least several percent of all recognized pregnancies. Among pregnancies that survive to term, chromosome abnormalities are a leading cause of developmental defects, failure to thrive in the newborn period, and intellectual disability. Mitotic nondisjunction in somatic cells also contributes to genetic disease. Nondisjunction soon after fertilization, either in the developing embryo or in extraembryonic tissues like the placenta, leads to chromosomal mosaicism that can underlie some medical conditions, such as a proportion of patients with Down syndrome. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 20). Elsevier Health Sciences. Kindle Edition.

At what stages of a dividing human cell are condensed chromosomes readily analyzed by microscope?

The condensed chromosomes of a dividing human cell are most readily analyzed at metaphase or prometaphase. At these stages, the chromosomes are visible under the microscope as a so-called chromosome spread; each chromosome consists of its sister chromatids, although in most chromosome preparations, the two chromatids are held together so tightly that they are rarely visible as separate entities. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 13-14). Elsevier Health Sciences. Kindle Edition.

What are the five stages of mitosis?

The process of mitosis is continuous, but five stages, illustrated in Figure 2-9, are distinguished: prophase, prometaphase, metaphase, anaphase, and telophase. • Prophase. This stage is marked by gradual condensation of the chromosomes, formation of the mitotic spindle, and formation of a pair of centrosomes, from which microtubules radiate and eventually take up positions at the poles of the cell. • Prometaphase. Here, the nuclear membrane dissolves, allowing the chromosomes to disperse within the cell and to attach, by their kinetochores, to microtubules of the mitotic spindle. • Metaphase. At this stage, the chromosomes are maximally condensed and line up at the equatorial plane of the cell. • Anaphase. The chromosomes separate at the centromere, and the sister chromatids of each chromosome now become independent daughter chromosomes, which move to opposite poles of the cell. • Telophase. Now, the chromosomes begin to decondense from their highly contracted state, and a nuclear membrane begins to re-form around each of the two daughter nuclei, which resume their interphase appearance. To complete the process of cell division, the cytoplasm cleaves by a process known as cytokinesis. There is an important difference between a cell entering mitosis and one that has just completed the process. A cell in G2 has a fully replicated genome (i.e., a 4n complement of DNA), and each chromosome consists of a pair of sister chromatids. In contrast, after mitosis, the chromosomes of each daughter cell have only one copy of the genome. This copy will not be duplicated until a daughter cell in its turn reaches the S phase of the next cell cycle (see Fig. 2-8). The entire process of mitosis thus ensures the orderly duplication and distribution of the genome through successive cell divisions. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 13). Elsevier Health Sciences. Kindle Edition.

What are the genetic consequences and medical relevance of homologous recombination?

The take-home lesson of this portion of the chapter is a simple one: the genetic content of each gamete is unique, because of random assortment of the parental chromosomes to shuffle the combination of sequence variants between chromosomes and because of homologous recombination to shuffle the combination of sequence variants within each and every chromosome. This has significant consequences for patterns of genomic variation among and between different populations around the globe and for diagnosis and counseling of many common conditions with complex patterns of inheritance (see Chapters 8 and 10). The amounts and patterns of meiotic recombination are determined by sequence variants in specific genes and at specific "hot spots" and differ between individuals, between the sexes, between families, and between populations (see Chapter 10). Because recombination involves the physical intertwining of the two homologues until the appropriate point during meiosis I, it is also critical for ensuring proper chromosome segregation during meiosis. Failure to recombine properly can lead to chromosome missegregation (nondisjunction) in meiosis I and is a frequent cause of pregnancy loss and of chromosome abnormalities like Down syndrome (see Chapters 5 and 6). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 18). Elsevier Health Sciences. Kindle Edition.

What is the difference between germ line and somatic cells? What are autosomes versus sex chromosomes? What are homologous chromosomes? What are alleles?

With the exception of cells that develop into gametes (the germline), all cells that contribute to one's body are called somatic cells (soma, body). The genome contained in the nucleus of human somatic cells consists of 46 chromosomes, made up of 24 different types and arranged in 23 pairs (Fig. 2-1). Of those 23 pairs, 22 are alike in males and females and are called autosomes, originally numbered in order of their apparent size from the largest to the smallest. The remaining pair comprises the two different types of sex chromosomes: an X and a Y chromosome in males and two X chromosomes in females. Central to the concept of the human genome, each chromosome carries a different subset of genes that are arranged linearly along its DNA. Members of a pair of chromosomes (referred to as homologous chromosomes or homologues) carry matching genetic information; that is, they typically have the same genes in the same order. At any specific locus, however, the homologues either may be identical or may vary slightly in sequence; these different forms of a gene are called alleles. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 4). Elsevier Health Sciences. Kindle Edition.

Is X inactivation in early female embryonic development random? What control complex / master regulatory locus is responsible for X inactivation?

X inactivation occurs very early in female embryonic development, and determination of which X will be designated the inactive X in any given cell in the embryo is a random choice under the control of a complex locus called the X inactivation center. This region contains an unusual ncRNA gene, XIST, that appears to be a key master regulatory locus for X inactivation. XIST (an acronym for inactive X [Xi]- specific transcripts) has the novel feature that it is expressed only from the allele on the inactive X; it is transcriptionally silent on the active X in both male and female cells. Although the exact mode of action of XIST is unknown, X inactivation cannot occur in its absence. The product of XIST is a long ncRNA that stays in the nucleus in close association with the inactive X chromosome. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 41). Elsevier Health Sciences. Kindle Edition.

What is each complex of DNA with core histones called?

complex of DNA with core histones is called a nucleosome (see Fig. 2-5), which is the basic structural unit of chromatin, and each of the 46 human chromosomes contains several hundred thousand to well over a million nucleosomes. A fifth histone, H1, appears to bind to DNA at the edge of each nucleosome, in the internucleosomal spacer region. The amount of DNA associated with a core nucleosome, together with the spacer region, is approximately 200 bp. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 7-8). Elsevier Health Sciences. Kindle Edition.

Does the 5' to 3' sequence of mRNA directly correspond to the 5' to 3' sequence of DNA or to the 3' to 5' sequence of DNA? (obviously except for the fact that U is substituted for T in RNA)

levels. As mentioned previously, it is the 3′ to 5′ strand of the DNA that serves as the template and is actually transcribed, but it is the 5′ to 3′ strand of DNA that directly corresponds to the 5′ to 3′ sequence of the mRNA (and, in fact, is identical to it except that U is substituted for T). Because of this correspondence, the 5′ to 3′ DNA strand of a gene (i.e., the strand that is not transcribed) is the strand generally reported in the scientific literature or in databases. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 30). Elsevier Health Sciences. Kindle Edition.

What state of the cell cycle is most of the cell's life spent?

A human being begins life as a fertilized ovum (zygote), a diploid cell from which all the cells of the body (estimated to be approximately 100 trillion in number) are derived by a series of dozens or even hundreds of mitoses. Mitosis is obviously crucial for growth and differentiation, but it takes up only a small part of the life cycle of a cell. The period between two successive mitoses is called interphase, the state in which most of the life of a cell is spent. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 11). Elsevier Health Sciences. Kindle Edition.

What is the major difference in regards to meiosis between males and females?

Both spermatogenesis and oogenesis require meiosis but have important differences in detail and timing that may have clinical and genetic consequences for the offspring. Female meiosis is initiated once, early during fetal life, in a limited number of cells. In contrast, male meiosis is initiated continuously in many cells from a dividing cell population throughout the adult life of a male. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 18). Elsevier Health Sciences. Kindle Edition.

How many letters of digital code exists in the human genome?

How does the 3-billion-letter digital code of the human genome guide the intricacies of human anatomy, physiology, and biochemistry to which Berg referred? The answer lies in the enormous amplification and integration of information content that occurs as one moves from genes in the genome to their products in the cell and to the observable expression of that genetic information as cellular, morphological, clinical, or biochemical traits— what is termed the phenotype of the individual.

What is the difference between G1 and G0 in the cell cycle? What is the S phase? Which phase forms the two sister chromatids? What holds the sister chromatids together? Where does DNA synthesis begin along chromosomes?

Immediately after mitosis, the cell enters a phase, called G1, in which there is no DNA synthesis (Fig. 2-8). Some cells pass through this stage in hours; others spend a long time, days or years, in G1. In fact, some cell types, such as neurons and red blood cells, do not divide at all once they are fully differentiated; rather, they are permanently arrested in a distinct phase known as G0 (" G zero"). Other cells, such as liver cells, may enter G0 but, after organ damage, return to G1 and continue through the cell cycle. The cell cycle is governed by a series of checkpoints that determine the timing of each step in mitosis. In addition, checkpoints monitor and control the accuracy of DNA synthesis as well as the assembly and attachment of an elaborate network of microtubules that facilitate chromosome movement. If damage to the genome is detected, these mitotic checkpoints halt cell cycle progression until repairs are made or, if the damage is excessive, until the cell is instructed to die by programmed cell death (a process called apoptosis). During G1, each cell contains one diploid copy of the genome. As the process of cell division begins, the cell enters S phase, the stage of programmed DNA synthesis, ultimately leading to the precise replication of each chromosome's DNA. During this stage, each chromosome, which in G1 has been a single DNA molecule, is duplicated and consists of two sister chromatids (see Fig. 2-8), each of which contains an identical copy of the original linear DNA double helix. The two sister chromatids are held together physically at the centromere, a region of DNA that associates with a number of specific proteins to form the kinetochore. This complex structure serves to attach each chromosome to the microtubules of the mitotic spindle and to govern chromosome movement during mitosis. DNA synthesis during S phase is not synchronous throughout all chromosomes or even within a single chromosome; rather, along each chromosome, it begins at hundreds to thousands of sites, called origins of DNA replication. Individual chromosome segments have their own characteristic time of replication during the 6- to 8-hour S phase. The ends of each chromosome (or chromatid) are marked by telomeres, which consist of specialized repetitive DNA sequences that ensure the integrity of the chromosome during cell division. Correct maintenance of the ends of chromosomes requires a special enzyme called telomerase, which ensures that the very ends of each chromosome are replicated. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 12). Elsevier Health Sciences. Kindle Edition.

Describe briefly the concept of chromatin architecture. Do epigenetic signals affect chromatin architecture therefore gene expression?

In contrast to the impression one gets from viewing the genome as a linear string of sequence (see Fig. 3-7), the genome adopts a highly ordered and dynamic arrangement within the space of the nucleus, correlated with and likely guided by the epigenetic and epigenomic signals just discussed. This three-dimensional landscape is highly predictive of the map of all expressed sequences in any given cell type (the transcriptome) and reflects dynamic changes in chromatin architecture at different levels (Fig. 3-10). First, large chromosomal domains (up to millions of base pairs in size) can exhibit coordinated patterns of gene expression at the chromosome level, involving dynamic interactions between different intrachromosomal and interchromosomal points of contact within the nucleus. At a finer level, technical advances to map and sequence points of contact around the genome in the context of three-dimensional space have pointed to ordered loops of chromatin that position and orient genes precisely, exposing or blocking critical regulatory regions for access by RNA pol II, transcription factors, and other regulators. Lastly, specific and dynamic patterns of nucleosome positioning differ among cell types and tissues in the face of changing environmental and developmental cues (see Fig. 3-10). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 35). Elsevier Health Sciences. Kindle Edition.

What is the ENCODE Project?

Increasing evidence points to a role for epigenetic changes in human disease in response to environmental or lifestyle influences. The dynamic and reversible nature of epigenetic changes permits a level of adaptability or plasticity that greatly exceeds the capacity of DNA sequence alone and thus is relevant both to the origins and potential treatment of disease. A number of large-scale epigenomics projects (akin to the original Human Genome Project) have been initiated to catalogue DNA methylation sites genome-wide (the so-called methylome), to evaluate CpG landscapes across the genome, to discover new histone variants and modification patterns in various tissues, and to document positioning of nucleosomes around the genome in different cell types, and in samples from both asymptomatic individuals and those with cancer or other diseases. These analyses are part of a broad effort (called the ENCODE Project, for Encyclopedia of DNA Elements) to explore epigenetic patterns in chromatin genome-wide in order to better understand control of gene expression in different tissues or disease states. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 33). Elsevier Health Sciences. Kindle Edition.

What is meiosis I also referred to as? What is a notable feature of meiosis I?

Meiosis I is also known as the reduction division because it is the division in which the chromosome number is reduced by half through the pairing of homologues in prophase and by their segregation to different cells at anaphase of meiosis I. Meiosis I is also notable because it is the stage at which genetic recombination (also called meiotic crossing over) occurs. In this process, as shown for one pair of chromosomes in Figure 2-14, homologous segments of DNA are exchanged between nonsister chromatids of each pair of homologous chromosomes, thus ensuring that none of the gametes produced by meiosis will be identical to another. The conceptual and practical consequences of recombination for many aspects of human genetics and genomics are substantial and are outlined in the Box at the end of this section. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 14). Elsevier Health Sciences. Kindle Edition.

Describe the process of meiosis.

Meiosis, the process by which diploid cells give rise to haploid gametes, involves a type of cell division that is unique to germ cells. In contrast to mitosis, meiosis consists of one round of DNA replication followed by two rounds of chromosome segregation and cell division (see meiosis I and meiosis II in Fig. 2-13). As outlined here and illustrated in Figure 2-14, the overall sequence of events in male and female meiosis is the same; however, the timing of gametogenesis is very different in the two sexes, as we will describe more fully later in this chapter. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 14). Elsevier Health Sciences. Kindle Edition.

Where are RNAs initially transcribed? Where are mature RNAs found? What are the gene sequences that are transcribed but not translated (aka untranslated regions)?

Rather, in the majority of genes, the coding sequences are interrupted by one or more noncoding regions (Fig. 3-4). These intervening sequences, called introns, are initially transcribed into RNA in the nucleus but are not present in the mature mRNA in the cytoplasm, because they are removed (" spliced out") In addition, the collection of coding exons in any particular gene is flanked by additional sequences that are transcribed but untranslated, called the 5′ and 3′ untranslated regions (see Fig. 3-4). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 25). Elsevier Health Sciences. Kindle Edition.

What is the simplest and most common of all polymorphisms? What are synonymous versus nonsynonymous SNPs?

The simplest and most common of all polymorphisms are single nucleotide polymorphisms (SNPs). A locus characterized by a SNP usually has only two alleles, corresponding to the two different bases occupying that particular location in the genome (see Fig. 4-1). As mentioned previously, SNPs are common and are observed on average once every 1000 bp in the genome. However, the distribution of SNPs is uneven around the genome; many more SNPs are found in noncoding parts of the genome, in introns and in sequences that are some distance from known genes. Nonetheless, there is still a significant number of SNPs that do occur in genes and other known functional elements in the genome. For the set of protein-coding genes, over 100,000 exonic SNPs have been documented to date. Approximately half of these do not alter the predicted amino acid sequence of the encoded protein and are thus termed synonymous, whereas the other half do alter the amino acid sequence and are said to be nonsynonymous. Other SNPs introduce or change a stop codon (see Table 3-1), and yet others alter a known splice site; such SNPs are candidates to have significant functional consequences. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 45). Elsevier Health Sciences. Kindle Edition.

What is an example of a highly specialized form of monoallelic gene expression (not random)? In contrast, what does random monoallelic expression typically result from?

A highly specialized form of monoallelic gene expression is observed in the genes encoding immunoglobulins and T-cell receptors, expressed in B cells and T cells, respectively, as part of the immune response. In contrast to this highly specialized form of DNA rearrangement, monoallelic expression typically results from differential epigenetic regulation of the two alleles. One well-studied example of random monoallelic expression involves the OR gene family described earlier (see Fig. 3-2). In this case, only a single allele of one OR gene is expressed in each olfactory sensory neuron; the many hundred other copies of the OR family remain repressed in that cell. Other genes with chemosensory or immune system functions also show random monoallelic expression, suggesting that this mechanism may be a general one for increasing the diversity of responses for cells that interact with the outside world. However, this mechanism is apparently not restricted to the immune and sensory systems, because a substantial subset of all human genes (5% to 10% in different cell types) has been shown to undergo random allelic silencing; these genes are broadly distributed on all autosomes, have a wide range of functions, and vary in terms of the cell types and tissues in which monoallelic expression is observed. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 38-39). Elsevier Health Sciences. Kindle Edition.

What are microRNAs (miRNAs)? What is their function? What percentage of protein-coding genes in the genome are miRNAs thought to control the activity of?

A particular class of small RNAs of growing importance are the microRNAs (miRNAs), ncRNAs of only approximately 22 bases in length that suppress translation of target genes by binding to their respective mRNAs and regulating protein production from the target transcript( s). Well over 1000 miRNA genes have been identified in the human genome; some are evolutionarily conserved, whereas others appear to be of quite recent origin during evolution. Some miRNAs have been shown to down-regulate hundreds of mRNAs each, with different combinations of target RNAs in different tissues; combined, the miRNAs are thus predicted to control the activity of as many as 30% of all protein-coding genes in the genome. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 26-27). Elsevier Health Sciences. Kindle Edition.

What is the molecular definition of a gene?

A range of features characterize human genes (see Fig. 3-4). In Chapters 1 and 2, we briefly defined gene in general terms. At this point, we can provide a molecular definition of a gene as a sequence of DNA that specifies production of a functional product, be it a polypeptide or a functional RNA molecule. A gene includes not only the actual coding sequences but also adjacent nucleotide sequences required for the proper expression of the gene— that is, for the production of normal mRNA or other RNA molecules in the correct amount, in the correct place, and at the correct time during development or during the cell cycle. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 25). Elsevier Health Sciences. Kindle Edition.

What are examples of histone modifications? Histone modification = class of epigenetic mechanism.

A second class of epigenetic signals consists of an extensive inventory of modifications to any of the core histone types, H2A, H2B, H3, and H4 (see Chapter 2). Such modifications include histone methylation, phosphorylation, acetylation, and others at specific amino acid residues, mostly located on the N-terminal "tails" of histones that extend out from the core nucleosome itself (see Fig. 3-8). These epigenetic modifications are believed to influence gene expression by affecting chromatin compaction or accessibility and by signaling protein complexes that— depending on the nature of the signal— activate or silence gene expression at that site. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 34-35). Elsevier Health Sciences. Kindle Edition.

What happens after telophase I of meiosis? What is the difference between interphase in meiosis versus mitosis?

After telophase of meiosis I, the two haploid daughter cells enter meiotic interphase. In contrast to mitosis, this interphase is brief, and meiosis II begins. The notable point that distinguishes meiotic and mitotic interphase is that there is no S phase (i.e., no DNA synthesis and duplication of the genome) between the first and second meiotic divisions. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 17-18). Elsevier Health Sciences. Kindle Edition.

What is a karyotype?

Although experts can often analyze metaphase chromosomes directly under the microscope, a common procedure is to cut out the chromosomes from a digital image or photomicrograph and arrange them in pairs in a standard classification (Fig. 2-11). The completed picture is called a karyotype. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 14). Elsevier Health Sciences. Kindle Edition.

What are two general types of gene?

Although the ultimate catalogue of human genes remains an elusive target, we recognize two general types of gene, those whose product is a protein and those whose product is a functional RNA. • The number of protein-coding genes— recognized by features in the genome that will be discussed in Chapter 3— is estimated to be somewhere between 20,000 and 25,000. In this book, we typically use approximately 20,000 as the number, and the reader should recognize that this is both imprecise and perhaps an underestimate. • In addition, however, it has been clear for several decades that the ultimate product of some genes is not a protein at all but rather an RNA transcribed from the DNA sequence. There are many different types of such RNA genes (typically called noncoding genes to distinguish them from protein-coding genes), and it is currently estimated that there are at least another 20,000 to 25,000 noncoding RNA genes around the human genome. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 5). Elsevier Health Sciences. Kindle Edition.

What are duplications involving substantial repetitive DNA segments of a chromosome called?

An important additional type of repetitive DNA found in many different locations around the genome includes sequences that are duplicated, often with extraordinarily high sequence conservation. Duplications involving substantial segments of a chromosome, called segmental duplications, can span hundreds of kilobase pairs and account for at least 5% of the genome. When the duplicated regions contain genes, genomic rearrangements involving the duplicated sequences can result in the deletion of the region (and the genes) between the copies and thus give rise to disease (see Chapters 5 and 6). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 11). Elsevier Health Sciences. Kindle Edition.

Does anaphase I differ from anaphase in mitosis? What is disjunction?

Anaphase of meiosis I again differs substantially from the corresponding stage of mitosis. Here, it is the two members of each bivalent that move apart, not the sister chromatids (contrast Fig. 2-14 with Fig. 2-9). The homologous centromeres (with their attached sister chromatids) are drawn to opposite poles of the cell, a process termed disjunction. Thus the chromosome number is halved, and each cellular product of meiosis I has the haploid chromosome number. The 23 pairs of homologous chromosomes assort independently of one another, and as a result, the original paternal and maternal chromosome sets are sorted into random combinations. The possible number of combinations of the 23 chromosome pairs that can be present in the gametes is 223 (more than 8 million). Owing to the process of crossing over, however, the variation in the genetic material that is transmitted from parent to child is actually much greater than this. As a result, each chromatid typically contains segments derived from each member of the original parental chromosome pair, as illustrated schematically in Figure 2-14. For example, at this stage, a typical large human chromosome would be composed of three to five segments, alternately paternal and maternal in origin, as inferred from DNA sequence variants that distinguish the respective parental genomes (Fig. 2-15). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 16-17). Elsevier Health Sciences. Kindle Edition.

What does the human genome consist of?

Appreciation of the importance of genetics to medicine requires an understanding of the nature of the hereditary material, how it is packaged into the human genome, and how it is transmitted from cell to cell during cell division and from generation to generation during reproduction. The human genome consists of large amounts of the chemical deoxyribonucleic acid (DNA) that contains within its structure the genetic information needed to specify all aspects of embryogenesis, development, growth, metabolism, and reproduction— essentially all aspects of what makes a human being a functional organism. Every nucleated cell in the body carries its own copy of the human genome, which contains, depending on how one defines the term, approximately 20,000 to 50,000 genes (see Box later). Genes, which at this point we consider simply and most broadly as functional units of genetic information, are encoded in the DNA of the genome, organized into a number of rod-shaped organelles called chromosomes in the nucleus of each cell. The influence of genes and genetics on states of health and disease is profound, and its roots are found in the information encoded in the DNA that makes up the human genome. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 3). Elsevier Health Sciences. Kindle Edition.

What is a locus (plural - loci)? What are alternative versions of a DNA sequence at a locus called?

As described in Chapter 2, a segment of DNA occupying a particular position or location on a chromosome is a locus (plural loci). A locus may be large, such as a segment of DNA that contains many genes, such as the major histocompatibility complex locus involved in the response of the immune system to foreign substances; it may be a single gene, such as the β-globin locus we introduced in Chapter 3; or it may even be just a single base in the genome, as in the case of a single nucleotide variant (see Fig. 2-6 and later in this chapter). Alternative versions of the DNA sequence at a locus are called alleles. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 43). Elsevier Health Sciences. Kindle Edition.

Why isn't there a simple one to one correspondence between genes and proteins?

As introduced briefly in Chapter 2, the product of protein-coding genes is a protein whose structure ultimately determines its particular functions in the cell. But if there were a simple one-to-one correspondence between genes and proteins, we could have at most approximately 20,000 different proteins. This number seems insufficient to account for the vast array of functions that occur in human cells over the life span. The answer to this dilemma is found in two features of gene structure and function. First, many genes are capable of generating multiple different products, not just one (see Fig. 3-1). This process, discussed later in this chapter, is accomplished through the use of alternative coding segments in genes and through the subsequent biochemical modification of the encoded protein; these two features of complex genomes result in a substantial amplification of information content. Indeed, it has been estimated that in this way, these 20,000 human genes can encode many hundreds of thousands of different proteins, collectively referred to as the proteome. Second, individual proteins do not function by themselves. They form elaborate networks, involving many different proteins and regulatory RNAs that respond in a coordinated and integrated fashion to many different genetic, developmental, or environmental signals. The combinatorial nature of protein networks results in an even greater diversity of possible cellular functions. Genes are located throughout the genome but tend to cluster in particular regions on particular chromosomes and to be relatively sparse in other regions or on other chromosomes. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 22). Elsevier Health Sciences. Kindle Edition.

There are protein-coding genes (ultimately code for a protein) and then there are noncoding RNA genes (ultimately code for RNA itself - doesn't translate to a protein). What is the purpose of noncoding RNA genes - give examples? How many ncRNA (non coding RNA) genes are there in comparison to protein coding genes?

As just discussed, many genes are protein coding and are transcribed into mRNAs that are ultimately translated into their respective proteins; their products comprise the enzymes, structural proteins, receptors, and regulatory proteins that are found in various human tissues and cell types. However, as introduced briefly in Chapter 2, there are additional genes whose functional product appears to be the RNA itself (see Fig. 3-1). These so-called noncoding RNAs (ncRNAs) have a range of functions in the cell, although many do not as yet have any identified function. By current estimates, there are some 20,000 to 25,000 ncRNA genes in addition to the approximately 20,000 protein-coding genes that we introduced earlier. Thus the collection of ncRNAs represents approximately half of all identified human genes. Chromosome 11, for example, in addition to its 1300 protein-coding genes, has an estimated 1000 ncRNA genes. Some of the types of ncRNA play largely generic roles in cellular infrastructure, including the tRNAs and rRNAs involved in translation of mRNAs on ribosomes, other RNAs involved in control of RNA splicing, and small nucleolar RNAs (snoRNAs) involved in modifying rRNAs. Additional ncRNAs can be quite long (thus sometimes called long ncRNAs, or lncRNAs) and play roles in gene regulation, gene silencing, and human disease. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 26). Elsevier Health Sciences. Kindle Edition.

What is the subtle difference between alternative splicing and RNA splicing?

As just discussed, when introns are removed from the primary RNA transcript by RNA splicing, the remaining exons are spliced together to generate the final, mature mRNA. However, for most genes, the primary transcript can follow multiple alternative splicing pathways, leading to the synthesis of multiple related but different mRNAs, each of which can be subsequently translated to generate different protein products (see Fig. 3-1). Some of these alternative events are highly tissue- or cell type- specific, and, to the extent that such events are determined by primary sequence, they are subject to allelic variation between different individuals. Nearly all human genes undergo alternative splicing to some degree, and it has been estimated that there are an average of two or three alternative transcripts per gene in the human genome, thus greatly expanding the information content of the human genome beyond the approximately 20,000 protein-coding genes. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 32). Elsevier Health Sciences. Kindle Edition.

How big is the mitochondrial DNA molecule and how many genes does it encode?

As mentioned earlier, a small but important subset of genes encoded in the human genome resides in the cytoplasm in the mitochondria (see Fig. 2-1). Mitochondrial genes exhibit exclusively maternal inheritance (see Chapter 7). Human cells can have hundreds to thousands of mitochondria, each containing a number of copies of a small circular molecule, the mitochondrial chromosome. The mitochondrial DNA molecule is only 16 kb in length (just a tiny fraction of the length of even the smallest nuclear chromosome) and encodes only 37 genes. The products of these genes function in mitochondria, although the vast majority of proteins within the mitochondria are, in fact, the products of nuclear genes. Mutations in mitochondrial genes have been demonstrated in several maternally inherited as well as sporadic disorders Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 8). Elsevier Health Sciences. Kindle Edition.

When staining chromosomes, what are the recognizable cytogenetic landmarks?

As stated earlier, there are 24 different types of human chromosome, each of which can be distinguished cytologically by a combination of overall length, location of the centromere, and sequence content, the latter reflected by various staining methods. The centromere is apparent as a primary constriction, a narrowing or pinching-in of the sister chromatids due to formation of the kinetochore. This is a recognizable cytogenetic landmark, dividing the chromosome into two arms, a short arm designated p (for petit) and a long arm designated q. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 14). Elsevier Health Sciences. Kindle Edition.

What is the structure of DNA?

Before the organization of the human genome and its chromosomes is considered in detail, it is necessary to review the nature of the DNA that makes up the genome. DNA is a polymeric nucleic acid macromolecule composed of three types of units: a five-carbon sugar, deoxyribose; a nitrogen-containing base; and a phosphate group (Fig. 2-2). The bases are of two types, purines and pyrimidines. In DNA, there are two purine bases, adenine (A) and guanine (G), and two pyrimidine bases, thymine (T) and cytosine (C). Nucleotides, each composed of a base, a phosphate, and a sugar moiety, polymerize into long polynucleotide chains held together by 5′-3′ phosphodiester bonds formed between adjacent deoxyribose units (Fig. 2-3A). In the human genome, these polynucleotide chains exist in the form of a double helix (Fig. 2-3B) that can be hundreds of millions of nucleotides long in the case of the largest human chromosomes. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 5-6). Elsevier Health Sciences. Kindle Edition.

What are potential sites of mutation in genetic disease that can interfere with the normal expression of a gene?

Both promoters and other regulatory elements (located either 5′ or 3′ of a gene or in its introns) can be sites of mutation in genetic disease that can interfere with the normal expression of a gene. These regulatory elements, including enhancers, insulators, and locus control regions, are discussed more fully later in this chapter. Some of these elements lie a significant distance away from the coding portion of a gene, thus reinforcing the concept that the genomic environment in which a gene resides is an important feature of its evolution and regulation. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 25). Elsevier Health Sciences. Kindle Edition.

How can one possibly quantify the relative level of transcription of all the genes (both protein-coding and noncoding) that are transcriptionally active in a cell?

By determining the sequences of all the RNA products— the transcriptome— in a population of cells, one can quantify the relative level of transcription of all the genes (both protein-coding and noncoding) that are transcriptionally active in those cells. Consider, for example, the collection of protein-coding genes. Although an average cell might contain approximately 300,000 copies of mRNA in total, the abundance of specific mRNAs can differ over many orders of magnitude; among genes that are active, most are expressed at low levels (estimated to be < 10 copies of that gene's mRNA per cell), whereas others are expressed at much higher levels (several hundred to a few thousand copies of that mRNA per cell). Only in highly specialized cell types are particular genes expressed at very high levels (many tens of thousands of copies) that account for a significant proportion of all mRNA in those cells. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 37). Elsevier Health Sciences. Kindle Edition.

What happens to the cell by the end of S phase? What happens during G2? What are the three phases that constitute interphase?

By the end of S phase, the DNA content of the cell has doubled, and each cell now contains two copies of the diploid genome. After S phase, the cell enters a brief stage called G2. Throughout the whole cell cycle, the cell gradually enlarges, eventually doubling its total mass before the next mitosis. G2 is ended by mitosis, which begins when individual chromosomes begin to condense and become visible under the microscope as thin, extended threads, a process that is considered in greater detail in the following section. The G1, S, and G2 phases together constitute interphase. In typical dividing human cells, the three phases take a total of 16 to 24 hours, whereas mitosis lasts only 1 to 2 hours (see Fig. 2-8). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 12). Elsevier Health Sciences. Kindle Edition.

What do regions of the genome with similar characteristics tend to do?

Chromosomes are not just a random collection of different types of genes and other DNA sequences. Regions of the genome with similar characteristics tend to be clustered together, and the functional organization of the genome reflects its structural organization and sequence. Some chromosome regions, or even whole chromosomes, are high in gene content (" gene rich"), whereas others are low (" gene poor") (Fig. 2-7). The clinical consequences of abnormalities of genome structure reflect the specific nature of the genes and sequences involved. Thus abnormalities of gene-rich chromosomes or chromosomal regions tend to be much more severe clinically than similar-sized defects involving gene-poor parts of the genome. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 8). Elsevier Health Sciences. Kindle Edition.

Describe the difference between a chromosome and chromatin. Describe how chromatin gives the appearance of beads on a string.

Chromosomes are not naked DNA double helices, however. Within each cell, the genome is packaged as chromatin, in which genomic DNA is complexed with several classes of specialized proteins. Except during cell division, chromatin is distributed throughout the nucleus and is relatively homogeneous in appearance under the microscope. When a cell divides, however, its genome condenses to appear as microscopically visible chromosomes. Chromosomes are thus visible as discrete structures only in dividing cells, although they retain their integrity between cell divisions. The DNA molecule of a chromosome exists in chromatin as a complex with a family of basic chromosomal proteins called histones. This fundamental unit interacts with a heterogeneous group of nonhistone proteins, which are involved in establishing a proper spatial and functional environment to ensure normal chromosome behavior and appropriate gene expression. Five major types of histones play a critical role in the proper packaging of chromatin. Two copies each of the four core histones H2A, H2B, H3, and H4 constitute an octamer, around which a segment of DNA double helix winds, like thread around a spool (Fig. 2-5). Approximately 140 base pairs (bp) of DNA are associated with each histone core, making just under two turns around the octamer. After a short (20- to 60-bp) "spacer" segment of DNA, the next core DNA complex forms, and so on, giving chromatin the appearance of beads on a string. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 7). Elsevier Health Sciences. Kindle Edition.

In regards to repetitive DNA sequences, what do satellite DNAs refer to?

Clustered repeated sequences constitute an estimated 10% to 15% of the genome and consist of arrays of various short repeats organized in tandem in a head-to-tail fashion. The different types of such tandem repeats are collectively called satellite DNAs, so named because many of the original tandem repeat families could be separated by biochemical methods from the bulk of the genome as distinct (" satellite") fractions of DNA. Tandem repeat families vary with regard to their location in the genome and the nature of sequences that make up the array. In general, such arrays can stretch several million base pairs or more in length and constitute up to several percent of the DNA content of an individual human chromosome. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 10). Elsevier Health Sciences. Kindle Edition.

What does DNA methylation refer to? Does extensive DNA methylation repress or promote gene expression? DNA methylation = class of epigenetic mechanism.

DNA methylation involves the modification of cytosine bases by methylation of the carbon at the fifth position in the pyrimidine ring (Fig. 3-9). Extensive DNA methylation is a mark of repressed genes and is a widespread mechanism associated with the establishment of specific programs of gene expression during cell differentiation and development. Typically, DNA methylation occurs on the C of CpG dinucleotides (see Fig. 3-8) and inhibits gene expression by recruitment of specific methyl-CpG- binding proteins that, in turn, recruit chromatin-modifying enzymes to silence transcription. The presence of 5-methylcytosine (5-mC) is considered to be a stable epigenetic mark that can be faithfully transmitted through cell division; however, altered methylation states are frequently observed in cancer, with hypomethylation of large genomic segments or with regional hypermethylation (particularly at CpG islands) in others (see Chapter 15). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 33). Elsevier Health Sciences. Kindle Edition.

What are pseudogenes? What is the difference between nonprocessed pseudogenes and processed pseudogenes?

DNA sequences that closely resemble known genes but are nonfunctional are called pseudogenes, and there are tens of thousands of pseudogenes related to many different genes and gene families located all around the genome. Pseudogenes are of two general types, processed and nonprocessed. Nonprocessed pseudogenes are thought to be byproducts of evolution, representing "dead" genes that were once functional but are now vestigial, having been inactivated by mutations in critical coding or regulatory sequences. In contrast to nonprocessed pseudogenes, processed pseudogenes are pseudogenes that have been formed, not by mutation, but by a process called retrotransposition, which involves transcription, generation of a DNA copy of the mRNA (a so-called cDNA) by reverse transcription, and finally integration of such DNA copies back into the genome at a location usually quite distant from the original gene. Because such pseudogenes are created by retrotransposition of a DNA copy of processed mRNA, they lack introns and are not necessarily or usually on the same chromosome (or chromosomal region) as their progenitor gene. In many gene families, there are as many or even more pseudogenes as there are functional gene members. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 26). Elsevier Health Sciences. Kindle Edition.

What is an example of miRNA gene mutation/deletion that leads to a disease?

Deletion of a cluster of miRNA genes on chromosome 13 leads to a form of Feingold syndrome, a developmental syndrome of skeletal and growth defects, including microcephaly, short stature, and digital anomalies. • Mutations in the miRNA gene MIR96, in the region of the gene critical for the specificity of recognition of its target mRNA( s), can result in progressive hearing loss in adults. Deletion of clusters of snoRNA (small nucleolar RNA) genes on chromosome 15 results in Prader-Willi syndrome, a disorder characterized by obesity, hypogonadism, and cognitive impairment Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 27). Elsevier Health Sciences. Kindle Edition.

During the cell cycle, chromosomes pass through stages of condensation and decondensation, what is the most decondensed state? What are solenoid fibers?

During the cell cycle, as we will see later in this chapter, chromosomes pass through orderly stages of condensation and decondensation. However, even when chromosomes are in their most decondensed state, in a stage of the cell cycle called interphase, DNA packaged in chromatin is substantially more condensed than it would be as a native, protein-free, double helix. Further, the long strings of nucleosomes are themselves compacted into a secondary helical structure, a cylindrical "solenoid" fiber (from the Greek solenoeides, pipe-shaped) that appears to be the fundamental unit of chromatin organization (see Fig. 2-5). The solenoids are themselves packed into loops or domains attached at intervals of approximately 100,000 bp (equivalent to 100 kilobase pairs [kb], because 1 kb = 1000 bp) to a protein scaffold within the nucleus. It has been speculated that these loops are the functional units of the genome and that the attachment points of each loop are specified along the chromosomal DNA. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 8). Elsevier Health Sciences. Kindle Edition.

How much genomic variation is expected between two randomly selected individuals across the globe?

Early estimates were that any two randomly selected individuals would have sequences that are 99.9% identical or, put another way, that an individual genome would carry two different versions (alleles) of the human genome sequence at some 3 to 5 million positions, with different bases (e.g., a T or a G) at the maternally and paternally inherited copies of that particular sequence position (see Fig. 2-6). Although many of these allelic differences involve simply one nucleotide, much of the variation consists of insertions or deletions of (usually) short sequence stretches, variation in the number of copies of repeated elements (including genes), or inversions in the order of sequences at a particular position (locus) in the genome (see Chapter 4). The total amount of the genome involved in such variation is now known to be substantially more than originally estimated and approaches 0.5% between any two randomly selected individuals. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 11). Elsevier Health Sciences. Kindle Edition.

The birth and development of genetics and genomics.

Few areas of science and medicine are seeing advances at the pace we are experiencing in the related fields of genetics and genomics. It may appear surprising to many students today, then, to learn that an appreciation of the role of genetics in medicine dates back well over a century, to the recognition by the British physician Archibald Garrod and others that Mendel's laws of inheritance could explain the recurrence of certain clinical disorders in families. During the ensuing years, with developments in cellular and molecular biology, the field of medical genetics grew from a small clinical subspecialty concerned with a few rare hereditary disorders to a recognized medical specialty whose concepts and approaches are important components of the diagnosis and management of many disorders, both common and rare. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 1). Elsevier Health Sciences. Kindle Edition.

Describe the fundamentals of gene expression - aka how information flows from gene to polypeptide. What is responsible for determining the spatial and temporal pattern of expression of a gene? Where does gene transcription initiate? What does RNA splicing refer to?

For genes that encode proteins, the flow of information from gene to polypeptide involves several steps (Fig. 3-5). Initiation of transcription of a gene is under the influence of promoters and other regulatory elements, as well as specific proteins known as transcription factors, which interact with specific sequences within these regions and determine the spatial and temporal pattern of expression of a gene. Transcription of a gene is initiated at the transcriptional "start" site on chromosomal DNA at the beginning of a 5′ transcribed but untranslated region (called the 5′ UTR), just upstream from the coding sequences, and continues along the chromosome for anywhere from several hundred base pairs to more than a million base pairs, through both introns and exons and past the end of the coding sequences. After modification at both the 5′ and 3′ ends of the primary RNA transcript, the portions corresponding to introns are removed, and the segments corresponding to exons are spliced together, a process called RNA splicing. After splicing, the resulting mRNA (containing a central segment that is now colinear with the coding portions of the gene) is transported from the nucleus to the cytoplasm, where the mRNA is finally translated into the amino acid sequence of the encoded polypeptide. Each of the steps in this complex pathway is subject to error, and mutations that interfere with the individual steps have been implicated in a number of inherited disorders (see Chapters 11 and 12). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 27). Elsevier Health Sciences. Kindle Edition.

What do geneticists call the single prevailing allele usually present in more than half of the individuals in a population? What do geneticists call the other versions of the gene that differ from the wild type?

For many genes, there is a single prevailing allele, usually present in more than half of the individuals in a population, that geneticists call the wild-type or common allele. (In lay parlance, this is sometimes referred to as the "normal" allele. However, because genetic variation is itself very much "normal," the existence of different alleles in "normal" individuals is commonplace. Thus one should avoid using "normal" to designate the most common allele.) The other versions of the gene are variant (or mutant) alleles that differ from the wild-type allele because of the presence of a mutation, a permanent change in the nucleotide sequence or arrangement of DNA. Note that the terms mutation and mutant refer to DNA, but not to the human beings who carry mutant alleles. The terms denote a change in sequence but otherwise do not carry any connotation with respect to the function or fitness of that change. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 43). Elsevier Health Sciences. Kindle Edition.

What is parent of origin imprinting? How is it distinguished from random forms of monoallelic expression? What role do imprinting control regions (imprinting centers) play?

For the examples just described, the choice of which allele is expressed is not dependent on parental origin; either the maternal or paternal copy can be expressed in different cells and their clonal descendants. This distinguishes random forms of monoallelic expression from genomic imprinting, in which the choice of the allele to be expressed is nonrandom and is determined solely by parental origin. Imprinting is a normal process involving the introduction of epigenetic marks (see Fig. 3-8) in the germline of one parent, but not the other, at specific locations in the genome. These lead to monoallelic expression of a gene or, in some cases, of multiple genes within the imprinted region. Imprinting takes place during gametogenesis, before fertilization, and marks certain genes as having come from the mother or father (Fig. 3-12). After conception, the parent-of-origin imprint is maintained in some or all of the somatic tissues of the embryo and silences gene expression on allele( s) within the imprinted region; whereas some imprinted genes show monoallelic expression throughout the embryo, others show tissue-specific imprinting, especially in the placenta, with biallelic expression in other tissues. The imprinted state persists postnatally into adulthood through hundreds of cell divisions so that only the maternal or paternal copy of the gene is expressed. Yet, imprinting must be reversible: a paternally derived allele, when it is inherited by a female, must be converted in her germline so that she can then pass it on with a maternal imprint to her offspring. Likewise, an imprinted maternally derived allele, when it is inherited by a male, must be converted in his germline so that he can pass it on as a paternally imprinted allele to his offspring (see Fig. 3-12). Control over this conversion process appears to be governed by specific DNA elements called imprinting control regions or imprinting centers that are located within imprinted regions throughout the genome; although their precise mechanism of action is not known, many appear to involve ncRNAs that initiate the epigenetic change in chromatin, which then spreads outward along the chromosome over the imprinted region. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 39). Elsevier Health Sciences. Kindle Edition.

What does the genetic code refer to? What is transcription versus translation?

Genetic information is stored in the DNA of the genome by means of a code (the genetic code, discussed later) in which the sequence of adjacent bases ultimately determines the sequence of amino acids in the encoded polypeptide. First, RNA is synthesized from the DNA template through a process known as transcription. The RNA, carrying the coded information in a form called messenger RNA (mRNA), is then transported from the nucleus to the cytoplasm, where the RNA sequence is decoded, or translated, to determine the sequence of amino acids in the protein being synthesized. The process of translation occurs on ribosomes, which are cytoplasmic organelles with binding sites for all of the interacting molecules, including the mRNA, involved in protein synthesis. Ribosomes are themselves made up of many different structural proteins in association with specialized types of RNA known as ribosomal RNA (rRNA). Translation involves yet a third type of RNA, transfer RNA (tRNA), which provides the molecular link between the code contained in the base sequence of each mRNA and the amino acid sequence of the protein encoded by that mRNA. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 23-24). Elsevier Health Sciences. Kindle Edition.

What is X chromosome inactivation? How does it lead to dosage compensation? Are females or males affected by X chromosome inactivation? What does a barr body distinguish?

Here we discuss the chromosomal and molecular mechanisms of X chromosome inactivation, the most extensive example of random monoallelic expression in the genome and a mechanism of dosage compensation that results in the epigenetic silencing of most genes on one of the two X chromosomes in females. In normal female cells, the choice of which X chromosome is to be inactivated is a random one that is then maintained in each clonal lineage. Thus females are mosaic with respect to X-linked gene expression; some cells express alleles on the paternally inherited X but not the maternally inherited X, whereas other cells do the opposite (Fig. 3-13). This mosaic pattern of gene expression distinguishes most X-linked genes from imprinted genes, whose expression, as we just noted, is determined strictly by parental origin. Although X inactivation is clearly a chromosomal phenomenon, not all genes on the X chromosome show monoallelic expression in female cells. Extensive analysis of expression of nearly all X-linked genes has demonstrated that at least 15% of the genes show biallelic expression and are expressed from both active and inactive X chromosomes, at least to some extent; a proportion of these show significantly higher levels of mRNA production in female cells compared to male cells and are interesting candidates for a role in explaining sexually dimorphic traits. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 39-40). Elsevier Health Sciences. Kindle Edition.

What is the central dogma of gene expression? What is a eukaryote versus a prokaryote? What are the main differences between RNA and DNA?

How does the genome specify the functional complexity and diversity evident in Figure 3-1? As we saw in the previous chapter, genetic information is contained in DNA in the chromosomes within the cell nucleus. However, protein synthesis, the process through which information encoded in the genome is actually used to specify cellular functions, takes place in the cytoplasm. This compartmentalization reflects the fact that the human organism is a eukaryote. This means that human cells have a nucleus containing the genome, which is separated by a nuclear membrane from the cytoplasm. In contrast, in prokaryotes like the intestinal bacterium Escherichia coli, DNA is not enclosed within a nucleus. Because of the compartmentalization of eukaryotic cells, information transfer from the nucleus to the cytoplasm is a complex process that has been a focus of much attention among molecular and cellular biologists. The molecular link between these two related types of information— the DNA code of genes and the amino acid code of protein— is ribonucleic acid (RNA). The chemical structure of RNA is similar to that of DNA, except that each nucleotide in RNA has a ribose sugar component instead of a deoxyribose; in addition, uracil (U) replaces thymine as one of the pyrimidine bases of RNA (Fig. 3-3). An additional difference between RNA and DNA is that RNA in most organisms exists as a single-stranded molecule, whereas DNA, as we saw in Chapter 2, exists as a double helix. The informational relationships among DNA, RNA, and protein are intertwined: genomic DNA directs the synthesis and sequence of RNA, RNA directs the synthesis and sequence of polypeptides, and specific proteins are involved in the synthesis and metabolism of DNA and RNA. This flow of information is referred to as the central dogma of molecular biology. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 23). Elsevier Health Sciences. Kindle Edition.

What does the term epigenetic mean? Does epigenetics focus on changes in gene function/expression or changes to the gene sequence itself?

In Chapter 2, we introduced general aspects of chromatin that package the genome and its genes in all cells. Here, we explore the specific characteristics of chromatin that are associated with active or repressed genes as a step toward identifying the regulatory code for expression of the human genome. Such studies focus on reversible changes in the chromatin landscape as determinants of gene function rather than on changes to the genome sequence itself and are thus called epigenetic or, when considered in the context of the entire genome, epigenomic (Greek epi-, over or upon). The field of epigenetics is growing rapidly and is the study of heritable changes in cellular function or gene expression that can be transmitted from cell to cell (and even generation to generation) as a result of chromatin-based molecular signals (Fig. 3-8). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 33). Elsevier Health Sciences. Kindle Edition.

What type of sequence elements can markedly alter the efficiency of transcription? How are enhancers different than promoters?

In addition to the sequences that constitute a promoter itself, there are other sequence elements that can markedly alter the efficiency of transcription. The best characterized of these "activating" sequences are called enhancers. Enhancers are sequence elements that can act at a distance from a gene (often several or even hundreds of kilobases away) to stimulate transcription. Unlike promoters, enhancers are both position and orientation independent and can be located either 5′ or 3′ of the transcription start site. Specific enhancer elements function only in certain cell types and thus appear to be involved in establishing the tissue specificity or level of expression of many genes, in concert with one or more transcription factors. In the case of the β-globin gene, several tissue-specific enhancers are present both within the gene itself and in its flanking regions. The interaction of enhancers with specific regulatory proteins leads to increased levels of transcription. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 31-32). Elsevier Health Sciences. Kindle Edition.

What is a chromosome disorder? How common are chromosome disorders in liveborn infants?

In chromosome disorders, the defect is due not to a single mistake in the genetic blueprint but to an excess or a deficiency of the genes located on entire chromosomes or chromosome segments. For example, the presence of an extra copy of one chromosome, chromosome 21, underlies a specific disorder, Down syndrome, even though no individual gene on that chromosome is abnormal. Duplication or deletion of smaller segments of chromosomes, ranging in size from only a single gene up to a few percent of a chromosome's length, can cause complex birth defects like DiGeorge syndrome or even isolated autism without any obvious physical abnormalities. As a group, chromosome disorders are common, affecting approximately 7 per 1000 liveborn infants and accounting for approximately half of all spontaneous abortions occurring in the first trimester of pregnancy. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 2). Elsevier Health Sciences. Kindle Edition.

What is the role of tRNAs in the cytoplasm? What are ribosomes made of?

In the cytoplasm, mRNA is translated into protein by the action of a variety of short RNA adaptor molecules, the tRNAs, each specific for a particular amino acid. These remarkable molecules, each only 70 to 100 nucleotides long, have the job of bringing the correct amino acids into position along the mRNA template, to be added to the growing polypeptide chain. Protein synthesis occurs on ribosomes, macromolecular complexes made up of rRNA (encoded by the 18S and 28S rRNA genes), and several dozen ribosomal proteins (see Fig. 3-5). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 28). Elsevier Health Sciences. Kindle Edition.

Is there allelic imbalance in gene expression? Or do alleles get expressed in comparable levels?

It was once assumed that genes present in two copies in the genome would be expressed from both homologues at comparable levels. However, it has become increasingly evident that there can be extensive imbalance between alleles, reflecting both the amount of sequence variation in the genome and the interplay between genome sequence and epigenetic patterns that were just discussed. Although most genes show essentially equivalent levels of biallelic expression, recent analyses of this type have demonstrated widespread unequal allelic expression for 5% to 20% of autosomal genes in the genome (Table 3-2). For most of these genes, the extent of imbalance is twofold or less, although up to tenfold differences have been observed for some genes. This allelic imbalance may reflect interactions between genome sequence and gene regulation; for example, sequence changes can alter the relative binding of various transcription factors or other transcriptional regulators to the two alleles or the extent of DNA methylation observed at the two alleles (see Table 3-2). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 37). Elsevier Health Sciences. Kindle Edition.

Does metaphase I differ from metaphase in mitosis?

Metaphase I begins, as in mitosis, when the nuclear membrane disappears. A spindle forms, and the paired chromosomes align themselves on the equatorial plane with their centromeres oriented toward different poles (see Fig. 2-14). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 16). Elsevier Health Sciences. Kindle Edition.

Describe a multifactorial disease with complex inheritance? What is the estimated impact of multifactorial disease?

Multifactorial disease with complex inheritance describes the majority of diseases in which there is a genetic contribution, as evidenced by increased risk for disease (compared to the general public) in identical twins or close relatives of affected individuals, and yet the family history does not fit the inheritance patterns seen typically in single-gene defects. Multifactorial diseases include congenital malformations such as Hirschsprung disease (Case 22), cleft lip and palate, and congenital heart defects, as well as many common disorders of adult life, such as Alzheimer disease (Case 4), diabetes, and coronary artery disease. There appears to be no single error in the genetic information in many of these conditions. Rather, the disease is the result of the combined impact of variant forms of many different genes; each variant may cause, protect from, or predispose to a serious defect, often in concert with or triggered by environmental factors. Estimates of the impact of multifactorial disease range from 5% in the pediatric population to more than 60% in the entire population. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 2). Elsevier Health Sciences. Kindle Edition.

Do genes that are constitutively expressed in most or all tissues (aka housekeeping genes) usually have the CAT and TATA boxes? What do promoter regions of many housekeeping genes contain a high proportion of? How does DNA methylation typically affect CpG islands?

Not all gene promoters contain the two specific elements just described. In particular, genes that are constitutively expressed in most or all tissues (so-called housekeeping genes) often lack the CAT and TATA boxes, which are more typical of tissue-specific genes. Promoters of many housekeeping genes contain a high proportion of cytosines and guanines in relation to the surrounding DNA (see the promoter of the BRCA1 breast cancer gene in Fig. 3-4). Such CG-rich promoters are often located in regions of the genome called CpG islands, so named because of the unusually high concentration of the dinucleotide 5′-CpG-3′ (the p representing the phosphate group between adjacent bases; see Fig. 2-3) that stands out from the more general AT-rich genomic landscape. Some of the CG-rich sequence elements found in these promoters are thought to serve as binding sites for specific transcription factors. CpG islands are also important because they are targets for DNA methylation. Extensive DNA methylation at CpG islands is usually associated with repression of gene transcription, as we will discuss further later in the context of chromatin and its role in the control of gene expression. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 30-31). Elsevier Health Sciences. Kindle Edition.

What is the TATA box? What is the function of the TATA box? What is the CAT box? What happens in mutations occur in either of these sequence elements?

One important promoter sequence found in many, but not all, genes is the TATA box, a conserved region rich in adenines and thymines that is approximately 25 to 30 bp upstream of the start site of transcription (see Figs. 3-4 and 3-7). The TATA box appears to be important for determining the position of the start of transcription, which in the β-globin gene is approximately 50 bp upstream from the translation initiation site (see Fig. 3-6). Thus in this gene, there are approximately 50 bp of sequence at the 5′ end that are transcribed but are not translated; in other genes, the 5′ UTR can be much longer and can even be interrupted by one or more introns. A second conserved region, the so-called CAT box (actually CCAAT), is a few dozen base pairs farther upstream (see Fig. 3-7). Both experimentally induced and naturally occurring mutations in either of these sequence elements, as well as in other regulatory sequences even farther upstream, lead to a sharp reduction in the level of transcription, thereby demonstrating the importance of these elements for normal gene expression. Many mutations in these regulatory elements have been identified in patients with the hemoglobin disorder β-thalassemia (see Chapter 11). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 30). Elsevier Health Sciences. Kindle Edition.

What is the difference between single-copy (unique DNA) versus repetitive DNA?

Only approximately half of the total linear length of the genome consists of so-called single-copy or unique DNA, that is, DNA whose linear order of specific nucleotides is represented only once (or at most a few times) around the entire genome. This concept may appear surprising to some, given that there are only four different nucleotides in DNA. But, consider even a tiny stretch of the genome that is only 10 bases long; with four types of bases, there are over a million possible sequences. And, although the order of bases in the genome is not entirely random, any particular 16-base sequence would be predicted by chance alone to appear only once in any given genome. Most of the estimated 20,000 protein-coding genes in the genome are represented in single-copy DNA. The rest of the genome consists of several classes of repetitive DNA and includes DNA whose nucleotide sequence is repeated, either perfectly or with some variation, hundreds to millions of times in the genome. Sequences in the repetitive DNA fraction contribute to maintaining chromosome structure and are an important source of variation between different individuals. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 10). Elsevier Health Sciences. Kindle Edition.

How does prophase during meiosis I differ from prophase during mitosis?

Prophase of meiosis I differs in a number of ways from mitotic prophase, with important genetic consequences, because homologous chromosomes need to pair and exchange genetic information. The most critical early stage is called zygotene, when homologous chromosomes begin to align along their entire length. The process of meiotic pairing— called synapsis— is normally precise, bringing corresponding DNA sequences into alignment along the length of the entire chromosome pair. The paired homologues— now called bivalents— are held together by a ribbon-like proteinaceous structure called the synaptonemal complex, which is essential to the process of recombination. After synapsis is complete, meiotic crossing over takes place during pachytene, after which the synaptonemal complex breaks down. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 14-16). Elsevier Health Sciences. Kindle Edition.

When DNA is transcribed to RNA, can the RNA sequence then be edited to change the nucleotide sequence of the mRNA? (this suggests that the central dogma principle may not always hold true)

Recent findings suggest that the conceptual principle underlying the central dogma— that RNA and protein sequences reflect the underlying genomic sequence— may not always hold true. RNA editing to change the nucleotide sequence of the mRNA has been demonstrated in a number of organisms, including humans. This process involves deamination of adenosine at particular sites, converting an A in the DNA sequence to an inosine in the resulting RNA; this is then read by the translational machinery as a G, leading to changes in gene expression and protein function, especially in the nervous system. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 32-33). Elsevier Health Sciences. Kindle Edition.

What does the anatomical structure of DNA allow for? What is the purpose of the primary structure of DNA?

The anatomical structure of DNA carries the chemical information that allows the exact transmission of genetic information from one cell to its daughter cells and from one generation to the next. At the same time, the primary structure of DNA specifies the amino acid sequences of the polypeptide chains of proteins, as described in the next chapter. DNA has elegant features that give it these properties. The native state of DNA, as elucidated by James Watson and Francis Crick in 1953, is a double helix (see Fig. 2-3B). The helical structure resembles a right-handed spiral staircase in which its two polynucleotide chains run in opposite directions, held together by hydrogen bonds between pairs of bases: T of one chain paired with A of the other, and G with C. The specific nature of the genetic information encoded in the human genome lies in the sequence of C's, A's, G's, and T's on the two strands of the double helix along each of the chromosomes, both in the nucleus and in mitochondria (see Fig. 2-1). Because of the complementary nature of the two strands of DNA, knowledge of the sequence of nucleotide bases on one strand automatically allows one to determine the sequence of bases on the other strand. The double-stranded structure of DNA molecules allows them to replicate precisely by separation of the two strands, followed by synthesis of two new complementary strands, in accordance with the sequence of the original template strands (Fig. 2-4). Similarly, when necessary, the base complementarity allows efficient and correct repair of damaged DNA molecules. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 6). Elsevier Health Sciences. Kindle Edition.

What is a major take-home lesson of this book that underscores the comparison of individual genomes?

The comparison of individual genomes underscores the first major take-home lesson of this book— every individual has his or her own unique constitution of gene products, produced in response to the combined inputs of the genome sequence and one's particular set of environmental exposures and experiences. As pointed out in the previous chapter, this realization reflects what Garrod termed chemical individuality over a century ago and provides a conceptual foundation for the practice of genomic and personalized medicine. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 3). Elsevier Health Sciences. Kindle Edition.

Describe the composition of genes in the human genome.

The composition of genes in the human genome, as well as the determinants of their expression, is specified in the DNA of the 46 human chromosomes in the nucleus plus the mitochondrial chromosome. Each human chromosome consists of a single, continuous DNA double helix; that is, each chromosome is one long, double-stranded DNA molecule, and the nuclear genome consists, therefore, of 46 linear DNA molecules, totaling more than 6 billion nucleotide pairs (see Fig. 2-1). Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 6-7). Elsevier Health Sciences. Kindle Edition.

What is a polymorphism? What are "private" alleles?

The frequency of different variants (mutants) can vary widely in different populations around the globe, as we will explore in depth in Chapter 9. If there are two or more relatively common varient (mutant) alleles (defined by convention as having an allele frequency > 1%) at a locus in a population, that locus is said to exhibit polymorphism (literally "many forms") in that population. Most variant (mutant) alleles, however, are not frequent enough in a population to be considered polymorphisms; some are so rare as to be found in only a single family and are known as "private" alleles. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 43). Elsevier Health Sciences. Kindle Edition.

What are the possible functional consequences of DNA mutations?

The functional consequences of DNA mutations, even those that change a single base pair, run the gamut from being completely innocuous to causing serious illness, all depending on the precise location, nature, and size of the mutation. For example, even a mutation within a coding exon of a gene may have no effect on how a gene is expressed if the change does not alter the primary amino acid sequence of the polypeptide product; even if it does, the resulting change in the encoded amino acid sequence may not alter the functional properties of the protein. Not all mutations, therefore, are manifest in an individual. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 44). Elsevier Health Sciences. Kindle Edition.

What is genomic medicine?

The human genome of any individual can now be studied in its entirety, rather than one gene at a time. These developments are making possible the field of genomic medicine, which seeks to apply a large-scale analysis of the human genome and its products, including the control of gene expression, human gene variation, and interactions between genes and the environment, to medical care. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 1). Elsevier Health Sciences. Kindle Edition.

How many possible triplet codon combinations are there? How many amino acids exist? What does it mean to say the genetic code is degenerate? What are the only two amino acids specified by a single, unique codon? How many stop codons exist? What is the start codon?

The key to translation is a code that relates specific amino acids to combinations of three adjacent bases along the mRNA. Each set of three bases constitutes a codon, specific for a particular amino acid (Table 3-1). In theory, almost infinite variations are possible in the arrangement of the bases along a polynucleotide chain. At any one position, there are four possibilities (A, T, C, or G); thus, for three bases, there are 43, or 64, possible triplet combinations. These 64 codons constitute the genetic code. Because there are only 20 amino acids and 64 possible codons, most amino acids are specified by more than one codon; hence the code is said to be degenerate. For instance, the base in the third position of the triplet can often be either purine (A or G) or either pyrimidine (T or C) or, in some cases, any one of the four bases, without altering the coded message (see Table 3-1). Leucine and arginine are each specified by six codons. Only methionine and tryptophan are each specified by a single, unique codon. Three of the codons are called stop (or nonsense) codons because they designate termination of translation of the mRNA at that point. Translation of a processed mRNA is always initiated at a codon specifying methionine. Methionine is therefore the first encoded (amino-terminal) amino acid of each polypeptide chain, although it is usually removed before protein synthesis is completed. The codon for methionine (the initiator codon, AUG) establishes the reading frame of the mRNA; each subsequent codon is read in turn to predict the amino acid sequence of the protein. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 29). Elsevier Health Sciences. Kindle Edition.

What are the three base anticodons of tRNA molecules complementary to? What direction are proteins synthesized in?

The molecular links between codons and amino acids are the specific tRNA molecules. A particular site on each tRNA forms a three-base anticodon that is complementary to a specific codon on the mRNA. Bonding between the codon and anticodon brings the appropriate amino acid into the next position on the ribosome for attachment, by formation of a peptide bond, to the carboxyl end of the growing polypeptide chain. The ribosome then slides along the mRNA exactly three bases, bringing the next codon into line for recognition by another tRNA with the next amino acid. Thus proteins are synthesized from the amino terminus to the carboxyl terminus, which corresponds to translation of the mRNA in a 5′ to 3′ direction. As mentioned earlier, translation ends when a stop codon (UGA, UAA, or UAG) is encountered in the same reading frame as the initiator codon. (Stop codons in either of the other unused reading frames are not read, and therefore have no effect on translation.) The completed polypeptide is then released from the ribosome, which becomes available to begin synthesis of another protein. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 29). Elsevier Health Sciences. Kindle Edition.

What are the stages of spermatogenesis?

The stages of spermatogenesis are shown in Figure 2-16. The seminiferous tubules of the testes are lined with spermatogonia, which develop from the primordial germ cells by a long series of mitoses and which are in different stages of differentiation. Sperm (spermatozoa) are formed only after sexual maturity is reached. The last cell type in the developmental sequence is the primary spermatocyte, a diploid germ cell that undergoes meiosis I to form two haploid secondary spermatocytes. Secondary spermatocytes rapidly enter meiosis II, each forming two spermatids, which differentiate without further division into sperm. In humans, the entire process takes approximately 64 days. The enormous number of sperm produced, typically approximately 200 million per ejaculate and an estimated 1012 in a lifetime, requires several hundred successive mitoses. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 18-19). Elsevier Health Sciences. Kindle Edition.

What is cytogenetics? When was the normal human chromosome number established?

The study of chromosomes, their structure, and their inheritance is called cytogenetics. The science of human cytogenetics dates from 1956, when it was first established that the normal human chromosome number is 46. Since that time, much has been learned about human chromosomes, their normal structure and composition, and the identity of the genes that they contain, as well as their numerous and varied abnormalities. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 4). Elsevier Health Sciences. Kindle Edition.

How identical is the sequence of nuclear DNA between two unrelated humans? What fraction is responsible for the genetically determined variability between individuals?

This chapter is one of several in which we explore the nature of genetically determined differences among individuals. The sequence of nuclear DNA is approximately 99.5% identical between any two unrelated humans. Yet it is precisely the small fraction of DNA sequence difference among individuals that is responsible for the genetically determined variability that is evident both in one's daily existence and in clinical medicine. Many DNA sequence differences have little or no effect on outward appearance, whereas other differences are directly responsible for causing disease. Between these two extremes is the variation responsible for genetically determined variability in anatomy, physiology, dietary intolerances, susceptibility to infection, predisposition to cancer, therapeutic responses or adverse reactions to medications, and perhaps even variability in various personality traits, athletic aptitude, and artistic talent. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 43). Elsevier Health Sciences. Kindle Edition.

Describe the difference between mitosis and meiosis in regards to somatic and germ line division.

To achieve these related but distinct forms of genome inheritance, there are two kinds of cell division, mitosis and meiosis. Mitosis is ordinary somatic cell division by which the body grows, differentiates, and effects tissue regeneration. Mitotic division normally results in two daughter cells, each with chromosomes and genes identical to those of the parent cell. There may be dozens or even hundreds of successive mitoses in a lineage of somatic cells. In contrast, meiosis occurs only in cells of the germline. Meiosis results in the formation of reproductive cells (gametes), each of which has only 23 chromosomes— one of each kind of autosome and either an X or a Y. Thus, whereas somatic cells have the diploid (diploos, double) or the 2n chromosome complement (i.e., 46 chromosomes), gametes have the haploid (haploos, single) or the n complement (i.e., 23 chromosomes). Abnormalities of chromosome number or structure, which are usually clinically significant, can arise either in somatic cells or in cells of the germline by errors in cell division. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 11). Elsevier Health Sciences. Kindle Edition.

What polymerase is responsible for initiating transcription of protein-coding genes? What direction does synthesis of the primary RNA transcript occur? What is the coding aka sense strand? What is the noncoding aka antisense strand? Is it the coding or noncoding strand that serves as the template strand?

Transcription of protein-coding genes by RNA polymerase II (one of several classes of RNA polymerases) is initiated at the transcriptional start site, the point in the 5′ UTR that corresponds to the 5′ end of the final RNA product (see Figs. 3-4 and 3-5). Synthesis of the primary RNA transcript proceeds in a 5′ to 3′ direction, whereas the strand of the gene that is transcribed and that serves as the template for RNA synthesis is actually read in a 3′ to 5′ direction with respect to the direction of the deoxyribose phosphodiester backbone (see Fig. 2-3). Because the RNA synthesized corresponds both in polarity and in base sequence (substituting U for T) to the 5′ to 3′ strand of DNA, this 5′ to 3′ strand of nontranscribed DNA is sometimes called the coding, or sense, DNA strand. The 3′ to 5′ strand of DNA that is used as a template for transcription is then referred to as the noncoding, or antisense, strand. Transcription continues through both intronic and exonic portions of the gene, beyond the position on the chromosome that eventually corresponds to the 3′ end of the mature mRNA. Whether transcription ends at a predetermined 3′ termination point is unknown. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 27-28). Elsevier Health Sciences. Kindle Edition.

Draw the cycle of condensation and decondensation as a chromosome proceeds through the cell cycle.

Unlike the chromosomes seen in stained preparations under the microscope or in photographs, the chromosomes of living cells are fluid and dynamic structures. During mitosis, the chromatin of each interphase chromosome condenses substantially (Fig. 2-12). When maximally condensed at metaphase, DNA in chromosomes is approximately 1/ 10,000 of its fully extended state. When chromosomes are prepared to reveal bands (as in Figs. 2-10 and 2-11), as many as 1000 or more bands can be recognized in stained preparations of all the chromosomes. Each cytogenetic band therefore contains as many as 50 or more genes, although the density of genes in the genome, as mentioned previously, is variable. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 14). Elsevier Health Sciences. Kindle Edition.

What are the three main types of genetic factors?

Virtually any disease is the result of the combined action of genes and environment, but the relative role of the genetic component may be large or small. Among disorders caused wholly or partly by genetic factors, three main types are recognized: chromosome disorders, single-gene disorders, and multifactorial disorders. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 2). Elsevier Health Sciences. Kindle Edition.

What are the stages of oogenesis?

Whereas spermatogenesis is initiated only at the time of puberty, oogenesis begins during a female's development as a fetus (Fig. 2-17). The ova develop from oogonia, cells in the ovarian cortex that have descended from the primordial germ cells by a series of approximately 20 mitoses. Each oogonium is the central cell in a developing follicle. By approximately the third month of fetal development, the oogonia of the embryo have begun to develop into primary oocytes, most of which have already entered prophase of meiosis I. The process of oogenesis is not synchronized, and both early and late stages coexist in the fetal ovary. Although there are several million oocytes at the time of birth, most of these degenerate; the others remain arrested in prophase I (see Fig. 2-14) for decades. Only approximately 400 eventually mature and are ovulated as part of a woman's menstrual cycle. After a woman reaches sexual maturity, individual follicles begin to grow and mature, and a few (on average one per month) are ovulated. Just before ovulation, the oocyte rapidly completes meiosis I, dividing in such a way that one cell becomes the secondary oocyte (an egg or ovum), containing most of the cytoplasm with its organelles; the other cell becomes the first polar body (see Fig. 2-17). Meiosis II begins promptly and proceeds to the metaphase stage during ovulation, where it halts again, only to be completed if fertilization occurs. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 19-20). Elsevier Health Sciences. Kindle Edition.

Whether a variant (mutant) allele is considered a polymorphism or not depends on what?

Whether a variant is formally considered a polymorphism or not depends entirely on whether its frequency in a population exceeds 1% of the alleles in that population, and not on what kind of mutation caused it, how large a segment of the genome is involved, or whether it has a demonstrable effect on the individual. The location of a variant with respect to a gene also does not determine whether the variant is a polymorphism. Although most sequence polymorphisms are located between genes or within introns and are inconsequential to the functioning of any gene, others may be located in the coding sequence of genes themselves and result in different protein variants that may lead in turn to distinctive differences in human populations. Still others are in regulatory regions and may also have important effects on transcription or RNA stability. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 45). Elsevier Health Sciences. Kindle Edition.

What are the three different levels we use to conceptually distinguish mutations?

• Alterations of the sequence of DNA, involving the substitution, deletion, or insertion of DNA, ranging from a single nucleotide up to an arbitrarily set limit of approximately 100 kb (gene or DNA mutations) -- focus of Chapter 4. • Mutations that leave chromosomes intact but change the number of chromosomes in a cell (chromosome mutations) -- focus of Chapter 5. • Mutations that change only a portion of a chromosome and might involve a change in the copy number of a subchromosomal segment or a structural rearrangement involving parts of one or more chromosomes (regional or subchromosomal mutations) -- focus of Chapter 6. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (p. 44). Elsevier Health Sciences. Kindle Edition.

What factors are considered in determining the gene expression profile of any particular cell or cell type in a given individual at a given time (whether in the context of the cell cycle, early development, or one's entire life span) and under a given set of circumstances (as influenced by environment, lifestyle, or disease)?

• The primary sequence of genes, their allelic variants, and their encoded products • Regulatory sequences and their epigenetic positioning in chromatin • Interactions with the thousands of transcriptional factors, ncRNAs, and other proteins involved in the control of transcription, splicing, translation, and post-translational modification • Organization of the genome into subchromosomal domains • Programmed interactions between different parts of the genome • Dynamic three-dimensional chromatin packaging in the nucleus All of these orchestrate in an efficient, hierarchical, and highly programmed fashion. Disruption of any one— due to genetic variation, to epigenetic changes, and/ or to disease-related processes— would be expected to alter the overall cellular program and its functional output. Nussbaum, Robert L.; McInnes, Roderick R.; Willard, Huntington F. Thompson & Thompson Genetics in Medicine E-Book (Thompson and Thompson Genetics in Medicine) (pp. 35-36). Elsevier Health Sciences. Kindle Edition.