Genetics Unit 3 chapter 10.3 through 12.5

piRNAs

-a more general mechanism that inhibits germ-line activity of both DNA transposons and retrotransposons probably exists in all animals. -this mechanism involves special small RNAs called piRNAs that block transcription of TEs and translation of TE transcripts.

fluorescent in situ hybridization (FISH)

-a technique that provides a convenient bridge between the low resolution of a karyotype and the ultra-high resolution of a complete genomic sequence -FISH allows investigators to find the locations of specific DNA sequences with respect to the chromosomes in a karyotype. -the fundamental basis of FISH is inherent in nucleotide complementarity. researchers first obtain cells in mitotic metaphase and then drop the cells onto a glass microscope slide. cells are then subjected to treatments that successively burst the cells open, spread the chromosomes apart, fix the chromosomes on the slide, and gently denature the chromosomal DNA in a way that preserves the overall chromosomal structure even though the double helixes separate into single strands at numerous points. in a separate reaction, the researchers label a purified DNA sequence with a fluorescent tag, making a DNA probe. the probe DNA is denatured into single strands by heating, and the probe is then hybridized to the chromosomes on the plate. the probe will bind only to chromosomal regions that are complementary in nucleotide sequence, and the researchers can identify these regions by looking in a fluorescence microscope. -in one use of FISH, the probe is a short, defined sequence such as a cDNA clone. the results are fluorescent spots showing the location of the corresponding gene in the genome.

transposable element

-any segment of DNA that evolves the ability to move from place to place within a genome is by definition a transposable element, regardless of its origin or function. -TEs dont have to be sequences that do something for the organism; they are regarded as primarily "selfish" parasitic entities carrying only info that allows their self-perpetuation. -Some TEs appear to have evolved functions that help their host. -range from 50 - 10,000 bp in length. -a TE can be present in a genome anywhere from one to hundreds of thousands of times.

chromatin

-by itself, DNA does not have the ability to fold up small enough to fit in the cell nucleus. for sufficient compaction, it depends on interactions with two categories of proteins: histones and nonhistone chromosomal proteins. -chromatin is the generic term for any complex of DNA and protein found in a cell's nucleus. a chromosome is a piece of chromatin that contains (prior to the S phase) a single DNA molecule and behaves as a unit during cell division -although chromatin is roughly 1/3 DNA, 1/3 histones, and 1/3 nonhistone proteins by weight, it also contains a significant amount of RNA

translocation heterozygote

-certain patterns of chromosome segregation during meiosis produce genetically unbalanced gametes that at fertilization become deleterious to the zygote -have two haploid sets of chromosomes that do not carry the same arrangement of genetic information. during prophase of the first meitotic division, the translocated chromosomes and their normal homologs assume a cruciform (cross-like) configuration in which four chromosomes pair to achieve a maximum of synapsis between similar regions. -depending on the arrangement of the four chromosomes on the metaphase plate, this notmal disjunction of homologs produces one of two equally likely patterns of segregation

additional challenges faced during eukaryotic cell replication (not faced in prokaryotic cells)

-eukaryotic cells have much more DNA than prokaryotic cells, all of which needs to be copied within the short span of a cell cycle. -the DNA replication machinery in eukaryotic cells must be able to operate even though the DNA is wrapped around nucleosomes. -eukaryotic chromosomes are linear rather than circular, and the ends of linear chromosomes are difficult to copy.

X chromosome reactivation

-germ line cells undergo the reverse of X inactivation, that is, X reactivation -in females, X reactivation usually occurs in the oogonia, the female germ-line cells that divide mitotically and whose daughters develop into the oocytes that subsequently undergo meiosis -reactivation of the previously inactivated X chromosomes in the oogonia ensures that every mature ovum (gamete) receives an active X

TEs in humans

-human genome harbors about 4 million TEs whose total length constitutes about 44% of the genome -most (about 90%) of the TEs in humans are retrotransposons -transposable element movement in the human genome can be detected by comparing the human genome sequence with that of our closest relative, the chimpanzee, while more recent TE activity can be detected by comparing individual human genome sequences. -studies show that since the time of our last common ancestor with the chimpanzee, no human DNA transposons have been mobile and only relatively few retrotransposons have moved. -the low rate of TE mobilization in humans is due in part to the accumulation of mutations in TE DNA sequences, and in part to control mechanisms that minimize their movement.

meiotic nondisjunction

-if homologous chromosomes do not separate during the first meiotic division, two of the resulting haploid gametes will carry both homologs, and two will carry neither. produces aneuploid zygotes, half trisomic, half monosomic -if meiotic nondisjunction occurs during meiosis II, only two of the four resulting gametes will be aneuploid -creates unbalanced gametes and thus causes aneuploidy in the progeny.

nucleosome as the fundamental unit of chromosome packaging

-in an electron micrograph of chromatin, the nucleosomes resemble beads on a string, with the beads having a diameter of about 100 A and the string a diameter of about 20 A (1 A = 0.1 nm). The 20 A string is DNA -each bead is a nucleosome containing roughly 160 bp of DNA wrapped around a core composed of eight histones (2 each of H2A, H2B, H3, H4). the 160 bp of DNA wrap twice around this core histone octamer. -an additional 40 bp form linker DNA, which connects one nucleosome with the next.

mechanisms that limit TE movement

-in germ-line cells, an intron in the primary transcript for transposase mRNA is sometimes spliced out and sometimes not. the mRNA with the intron removed encodes transposase, while the alternative splice form of the mRNA that retains the intron encodes a smaller repressor polypeptide. repressor protein inhibits P element transposition by competing with transposase for binding to the transposon inverted repeats -in somatic cells, the intron is never removed; only repressor is produced (not transposase) and so P elements do not mobilize in the soma.

spectral karyotyping

-in this second variation of FISH, the probes are made from multiple DNAs that originated from positions scattered along the length of individual chromosomes. the probe for chromosome 1 is labeled with a mix of fluorescent tags that together glow one color, and so forth, so that each of the 24 human chromosomes in a SKY karyotype can be recognized easily by its color. -both of these FISH techniques remain important for characterizing chromosomal rearrangements such as deletions, duplications, inversions, and translocations that may cause genetic diseases.

gene mutations caused by TEs

-insertion of a TE near or within a gene can affet gene expression and change phenotype -one way active TEs in humans are identified is when their movement generates disease alleles. retrotransposon insertion mutations causing nearly 100 human diseases are known -a TE's effect on a gene depends on what the element is and where it inserts within or near the gene. -if an element lands within a protein-coding exon, the additional DNA may shift the reading frame or supply an in-frame stop codon that truncates the polypeptide -if the element falls in an intron, it could diminish the efficiency of splicing -TEs that land within exons or introns may also provide a transcription stop signal that prevents transcription of gene sequences downstream of the insertion site. -insertions into regions required for transcription, such as promoters, can influence the amount of gene product made in particular tissues at particular times during development.

Histone H1

-lies outside the core, associating with DNA entering and leaving the nucleosome. when investigators use specific chemical reagents to remove H1 from the chromatin, some DNA unwinds from each nucleosome, but the nucleosomes do not fall apart; about 140 bp remain wrapped around each core.

X inactivation center (XIC)

-mammals compensate for the difference in dosage of X-linked genes between males and females by randomly inactivating one of the two X chromosomes. -the inactive X chromosomes, or Barr Bodies, are examples of facultative heterochromatin: an entire X chromosome becomes nearly completely heterochromatic in some cells, while other copies of this same X chromosome remain euchromatic in other cells. only those few genes present in the pseudoautosomal regions of the X chromosome that has become a Barr body are available for transcription. -human X chromosome contain a 450 kb region of DNA called the XIC that mediates dosage compensation. when XIC was transferred to an autosome, that autosome became a Barr body -most important gene in the XIC is called Xist (X inactive specific transcript). the Xist gene product is an unusually long (about 17 kb) noncoding RNA (ncRNA) that, unlike most transcripts, never leaves the nucleus and is never translated into a protein. -Xist is transcribed stably only from the future inactive X chromosome, and it is the Xist ncRNA that triggers inactivation of the X chromosome from which it is transcribed. -Xist ncRNA coats the X chromosome that produces it. the Xist ncRNA then recruits histone-modifying enxymes to this X chromosome. the enzymes methylate and deacetylate the histone tails in the nucleosomes of this chromosome, helping to condense it into a Barr body.

cells that produce telomerase

-most differentiated somatic cells in humans make very little if any telomerase, and their chromosomes shorten during every cell generation. after 30-50 cell generations, the chromosomes begin to lose essential genes from their ends; the cells start to show signs of senescence and then die. lack of telomerase thus ensures that differentiated somatic cells have a finite lifespan -germ line cells do express telomerase, and thus maintain their chromosomal ends through repeated rounds of DNA replication without the loss of genes -stem cells, which allow tissue renewal (such as the continual production of blood cells), are a kind of somatic cell that makes telomerase, thus having the potential to reproduce for many generations, if not forever. -second class of somatic cells that produce telomerase are tumor cells: somatic cells gone awry that can divide indefinitely, becoming seemingly immortal. high telomerase activity is a characteristic of many tumor cells

phenotypic effects of duplications

-most duplications have no obvious phenotypic consequences bc an additional dose of most genes does not affect normal cellular or tissue physiology -some do have phenotypic consequences for visible traits or survival: -certain phenotypes may be particularly sensitive to an increase in the number of copies of a particular gene or set of genes -more rarely, a gene near one of the borders of a duplication has altered expression bc it is now found in a new chromosomal environment that does not exist in a wild-type chromosome

phenotypic effects of reciprocal translocation

-most individuals are phenotypically normal bc they have neither lost nor gained genetic material -as with inversions, however, if one of the translocation breakpoints occurs near or within a gene, that gene's function may change or be destroyed. -reciprocal translocations may result in decreased fertility

phenotypic effects of inversions

-most inversions do not result in an abnormal phenotype, bc even though they alter the order of genes along the chromosome, they do not add or remove DNA and therefore do not change the identity or number of genes. -however, if one end of an inversion lies within the DNA of a gene, a loss-of-function mutation in that gene will occur bc the inversion separates the two parts of the gene, relocating one part to a distant region of the chromosome. -inversions can also produce unusual phenotypes by moving genes residing near the inversion breakpoints to new chromosomal environments that alter their normal expression. -inversions that reposition genes normally found in euchromatin to a position near a region of heterochromatin can also produce an unusual phenotype.

DNA transposons: Structure and Movement

-most transposons contain inverted repeats at their ends and encode a transposase enzyme that recognizes these inverted repeats -the transposase cuts at the borders between the transposon and adjacent genomic DNA, and it also helps the excised transposon integrate at a new site -transposase-catalyzed integration of P elements creates a duplication of 8 bp present at the new target site. -a gap remains when transposons are excised from their original position. -after exonucleases widen the gap, cells repair the gap using related DNA sequences as templates. -depending on whether the template contains or lacks a P element, the transposon will appear to remain at, or to be excised from, its original location

syntenic segments

-mouse chromosome 1 contains large blocks of sequences found on human chromosomes. these blocks represent syntenic segments in which the identity, order, and transcriptional direction of the genes are almost exactly the same in the two genomes.

instability of TE insertion mutations

-mutations caused by TE insertion are stable if an end of the element is damaged during mobilization, rendering the TE unmovable, or if elements encoding the mobilization proteins are no longer present in the genome. -otherwise, TE insertion mutations can be unstable: the TE can remobilize, usually resulting in reversion of the mutant allele to wild type.

lysine acetylation

-one of the best understood of these histone tail modifications is the addition of acetyl groups to specific lysines (acetylation) -lysine acetylation, accomplished by a family of enzymes called histone acetyl transferases (HATs), "opens" chromatin by preventing the close packing of nucleosomes. Histone acetylation thus favors the expression of genes in euchromatic regions, as their promoters are now accessible to RNA polymerase and its associated proteins. -the acetylated lysines on histone tails serve as binding sites for HAT enzymes, thus facilitating the spreading of histone acetylation to neighboring nucleosomes -histone deacetylase enzymes that remove the acetyl groups reverse the process, resulting in "closed" chromatin and repressed transcription

chromatin remodeling complexes

-one type of chromatin modulator consists of multisubunit remodeling complexes that use the energy of ATP hydrolysis to alter nucleosome positioning -other chromatin modulators chemically modify the tails of the histones in the nucleosome core -chromatin changes accomplished by both mechanisms expose the previously hidden promoter, allowing its recognition by RNA polymerase and thus facilitating the gene's transcriptional activation -differentiated cells have specific patterns of chromatin configuration and gene expression that persist after the cells divide by mitosis.

histones

-relatively small proteins with a preponderance of the basic, positively charged amino acids lysine and arginine. the histones' strong positive charge enables them to bind to and neutralize the negatively charged DNA throughout the chromatin. -histones make up half of all chromatin protein by weight, and are classified into 5 types of molecules: H1, H2A, H2B, H3, H4 -all 5 types of histones appear throughout the chromatin of nearly all diploid eukaryotic cells, and they are very similar in all eukaryotes. that histones have changed so little throughout evolution underscores the importance of their contribution to chromatin structure.

chromosomal rearrangements caused by TEs

-retrotransposons and transposons can trigger spontaneous chromosomal rearrangements other than transpositions in several ways -two copies of the same TE can pair with each other aberrantly and cross over to generate all kinds of chromosomal rearrangements. -other rearrangements result not from recombination between TEs, but rather from the process of transposition itself. mistakes can occur during transposition events that cause deletion or duplication of chromosomal material adjacent to the TE.

levels of chromosome compaction: nucleosome

-status: confirmed by crystal structure -what it accomplishes: condenses naked DNA 7-fold to a 100 A fiber

levels of chromosome compaction: supercoiling

-status: hypothetical model (although the 300 A fiber predicted by the model has been seen in the electron microscope) -what is accomplishes: causes additional 6-fold compaction (6 nucleosomes per turn), achieving a 40- to 50-fold condensation relative to naked DNA -whereas the 100 A fiber is one nucleosome in width, the 300 A fiber appears to be 3 beads wide. -histone H1 likely plays a special role in formation of the superhelix, bc removal of some H1 causes the 300 A to unwind to 100 A, while adding back H1 reverses this process. -although electron microscopists can actually see the 300 A fiber, they do not know its exact structure. higher levels of compaction are even less well understood.

levels of chromosome compaction: radial loop-scaffold

-status: hypothetical model (preliminary experimental support exists for this model) -what it accomplishes: through progressive compaction of 300 A fiber, condenses DNA to rodlike mitotic chromosomes that are 10,000 times more compact than naked DNA -progressive levels of chromosome compaction involving nucleosome formation, nucleosome supercoiling into the 300 A fiber, looping of the fibers, gathering of loops into rosettes, and rosette compression have the potential to give rise to the highly condensed, rodlike shapes we see as mitotic chromosomes. -several nonhistone proteins bind to chromatin every 60-100 kb and tether the 300 A fiber into structural loops; the loops are gathered into rosettes, the centers of white are compressed into a compact bundle.

histone tails

-the N-terminal regions of the four core histones--H2A, H2B, H3, H4-- form tails that extend outward from the nucleosome. enzymes can add several different kinds of chemical groups (among others, methyl groups, ethyl groups, phosphate groups, and ubiquitin) to various amino acids along these tails, while other enzymes can remove groups that were added previously. such modifications of these histone tails can influence the packing of nucleosomes, and the modified tails can also serve as platforms to which chromatin modifier proteins can bind. the histone tails of a nucleosome core potentially could be modified in more than 100 ways.

telomeres

-the linear chromosomes of eukaryotic cells terminate at both ends in protective caps called telomeres. composed of special DNA sequences associated with specific proteins, these caps contain no genes but are crucial in preserving the structural integrity of each chromosome -telomeres and an enzyme called telomerase provide a countermeasure to the limitation of DNA polymerase-- the fact that DNA polymerase cannot reconstruct the complete 5' end of a chromosome bc it moves in the 5' to 3' direction, and the primer that it was bound to is released, leaving a tail at the 5' end of every chromosome that is not copied. -telomeres consist of particular repetitive DNA sequences that do not encode proteins. human telomeres consist of the base sequence 5' TTAGGG 3' (read on one strand) repeated 250-1500 times. the number of repeats varies with the cell type; sperm cells have the longest telomeres. -the close similarities of these repeated sequences across phyla suggests that they perform a vital function that emerged in the earliest stages of the evolutionary line leading to eukaryotic organisms.

nonhistone chromosomal proteins

-the remaining half of the mass of protein in eukaryotic cell chromatin consists of thousands of different kinds of ____. -the chromatin of a diploid genome contains from 200- 2,000,000 molecules of each kind of nonhistone protein. -this large variety of proteins fulfills many different functions. -some play a purely structural role, helping to package DNA into more complex structures. the proteins that form the structural backbone, or scaffold, of the chromosome fall into this category -other nonhistone proteins, such as DNA polymerase, are active in replication -others are critical for chromosome segregation: ex- the motor proteins of kinetochores help move chromosomes along the spindle apparatus and thus expedite the transport of chromosomes from parent to daughter cells during mitosis and meiosis. -by far the largest class of nonhistone proteins comprises those which foster or regulate transcription and RNA processing during gene expression

idiograms

-the reproducibility of banding patterns means that geneticists can designate the chromosomal location of a gene by describing its position in relation to the bands on the p (short) or q (long) arm of a particular chromosome. the p and q arms are subdivided into regions, and within each region, the dark and light bands are numbered consecutively. diagrams of the banding patterns are called ____

heterochromatin

-this type of chromatin organization is widespread in genomes and is correlated with the strong suppression of gene expression. -in cells stained with certain DNA-binding chemicals, some chromosomal regions appear much darker than others. darker regions are called heterochromatin, and lighter regions are called euchromatin. -the much tighter packing of nucleosomes in heterochromatic regions means that the genes present in those regions are silenced. it is so tightly packed that the enzymes required for transcription of the few genes it contains cannot access the correct DNA sequences -most heterochromatin in highly condensed chromosomes is found in regions flanking the centromere -a high proportion of regions of heterochromatin consists of long stretches of simple repetitive sequences like SSRs. -heterochromatin regions are also repositories for many transposable elements--segments of DNA that move around the genome. -repetitive DNAs and transposable elements together constitute more than half of most genomes; their sequestration in transcriptionally inactive heterochromatin provides organisms with a way to minimize the effects of such 'junk' DNA on normal cellular physiology

Retrotransposons move via RNA intermediates

-transposition of a retrotransposon begins with its transcription by RNA polymerase into an RNA that encodes a reverse-transcriptase-like enzyme. -this enzyme can copy RNA into a single strand of cDNA and then use that single DNA strand as a template for producing double-stranded cDNA -many retrotransposons also encode polypeptides other than reverse transcriptase. -some retrotransposons have a poly-A tail at the 3' end of the RNA-like DNA strand, a configuration reminiscent of mRNA molecules.

G bands

-various staining techniques reveal a characteristic banding pattern, size, and shape for each metaphase chromosome, establishing a karyotype. -in G-banding, chromosomes are first gently heated and then exposed to Giemsa stain; this DNA dye preferentially darkens certain regions to produce alternating dark and light G bands. -each G-band is a very large segment of DNA from 1 to 10 Mb in length, containing many loops. -the biochemical basis of banding is not yet understood. most molecular geneticists think the bands produced by Giesma staining probably reflect an uneven packaging of loops determined in some way by the spacing and density of short, repetitive DNA sequences along the chromosomes -every time a chromosome replicates, its banding pattern is faithfully reproduced. they are therefore an intrinsic property of each chromosome, initially determined by the DNA sequence itself.

DNase hypersensitive site

-when a previously inactive gene prepares for transcription during a later step of cellular differentiation, the promoter region is observed to change from a DNase resistant site to a DNase hypersensitive site. -the reason is that transcription regulatory proteins (transcription factors) bind DNA at nearby enhancers, and recruit proteins that reorganize the chromatin in the vicinity. these newly recruited proteins remove the promoter-blocking nucleosomes or reposition them in relation to the gene

gene relocation due to transposition

-when two copies of a DNA transposon are found in nearby but not identical locations on the same chromosome, the inverted repeats at the outside ends of the two transposons are positioned with respect to each other just like the inverted repeats of a single transposon. -if transposase acts on this pair of inverted repeats during transposition, it allows the entire region between them to move as one giant transposon, mobilizing and relocating any genes the region contains.

transposase

DNA between the transposon's inverted repeats commonly contains a gene encoding a transposase, a protein that catalyzes transposition through its recognition of those repeats. the steps resulting in transposition include excision of the transposon from its original genomic position and integration into a new location

barrier insulators

DNA elements which block the spread of heterochromatin. the exact mechanism by which they work is unclear, but current models suggest that these are DNA sites that recruit enzymes that modify histone proteins. -they either attract HAT enzymes or demethylase enzymes that reverse K9 methylation

Steps in eukaryotic DNA replication

DNA replication is only one step in chromosome duplication. the complex process also includes the synthesis and incorporation of histone and nonhistone proteins to regenerate nucleosomes and chromatin structure. process works something like this: - As DNA replication takes place, nucleosomes assemble rapidly on newly formed daughter DNA molecules. the "new" nucleosomes are a mixture of old and newly formed histones, distributed randomly on the two daughter DNA molecules. -the synthesis and transport of histones must be tightly coordinated with DNA synthesis because the nascent DNA becomes incorporated into nucleosomes within minutes of its formation -histone modifications are labile; they become lost during DNA replication so that new nucleosomes do not have the modifications found in the chromatin of the parental cell. -just after replication, chromatin formed from new nucleosomes is open. a brief window of opportunity thus exists for transcription regulatory proteins in the nucleus to bind to the daughter DNA molecules. these proteins then recruit histone-modifying enzymes, recreating the chromatin structure of the parental chromosome even though the histone modifications were briefly lost when the DNA was replicated. -the replication fork disassembles the nucleosomes it encounters in the parental chromosome. new nucleosomes start assembling immediately after the replication fork passes. first, a tetramer containing two molecules each of histones H3 and H4 associates with DNA to form a half nucleosome, followed by two dimers each containing one molecule of H2A and one of H2B. the new nucleosomes can contain various random combinations of H3/H4 tetramers and H2A/H2B dimers that were either newly synthesized or that were previously found in parental nucleosomes

transposable elements

DNA sequences whose copies move from place to place, so that a single genome may accumulate hundreds of thousands of copies of such an element -crossovers between repeats of the same sequence at two locations on the same chromosome can result in a deletion if the repeats are in the same orientation, or an inversion if the repeats are in opposite orientations. -if two homologous chromosomes misalign at repeated sequences and cross over, the result may be a duplication and a deletion. -crossovers at a repeated sequence on two nonhomologous chromosomes generate reciprocal translocations

multicolor banding

FISH probes specific for particular regions of chromosomes generate "chromosome barcodes" -multicolor banding reveals the presence and nature of a deletion in a human chromosome

differences between the mechanisms by which poly-A-containing and LTR-containing retrotransposons move

LTR-containing: -translation of the pol gene in the retrotransposon transcript produces an enzyme with reverse transcriptase and endonuclease activity. -the enzyme initiates the process of converting retrotransposon RNA into a double stranded cDNA, and also cleaves a genomic DNA target site for insertion of the TE cDNA poly-A containing: -these TEs mobilize through a more complex mechanism that involves not only reverse transcriptase, but another retrotransposon-encoded protein called ORF1

HERVs

LTR-type retrotransposons that, in addition to a pol gene, can include gag and env genes encoding retroviral coat proteins. -structure contains LTR on both ends, as well as gag, pol, and env genes -length is 1-11 kb -in humans, there are 600,000 and they make up 8% of the human genome.

Transposons (or DNA transposons)

TEs that move their DNA directly without the requirement of an RNA intermediate -their ends are inverted repeats of each other; a sequence of base pairs at one end is present in mirror image at the other end. inverted repeat is usually 10-200 bp long -2 to 3 kb in length -in humans, there are 400,000 and they make up 3% of the human genome

retrotransposons

TEs that transpose via reverse transcription of an RNA intermediate

cohesin

a highly conserved, multisubunit protein complex called cohesin acts as the glue that holds sister chromatids together during mitosis and meiosis until segregation takes place -cohesin encircles the two double helixes of the sister chromatids to keep them together. -cohesin rings are scattered along the length of the chromosome, but they are found in particularly high concentrations in the vicinity of centromeric heterochromatin -during anaphase, a proteolytic enzyme called separase cleaves the cohesion complexes, allowing the sister chromatids to separate and move to opposite spindle poles -in meiosis, sister chromatids must stay together during meiosis I and then separate during meiosis II. cells solve this problem by making cohesin complexes with a meiosis-specific subunit that can interact with a protein called shugoshin, which protects the cohesin at the centromere from being cleaved by separase. upon entering meiosis II, shugoshin is removed, and separase can not cleave the centromeric cohesin at anaphase II, allowing sister chromatids to segregate to opposite poles. -shugoshin does not protect cohesin along the arms of the sister chromatids. thus, at anaphase of meiosis I, the cohesin along the arms of the sister chromatids is cleaved, while the centromere is not. cohesin along the arms is the glue keeping homologous chromosomes together while the spindle tries to pull them apart during metaphase. cleavage of the arm cohesin is therefore essential to allow the homologous chromosomes to segregate to oppposite spindle poles during anaphase of meiosis I.

nucleosome

a structural unit of a eukaryotic chromosome that consists of a length of DNA coiled around a core of histone proteins

rearrangement breakpoints

all rearrangement types will juxtapose DNA sequences that would not normally be connected. the novel sequences at these junctures that are found in the data analysis define the precise rearrangement breakpoints-- the base pairs at which the rearranged region begins and ends. knowledge of these breakpoints is critical for understanding which genes could be responsible for phenotypes associated with the rearrangement -advanced FISH techniques can reveal chromosome rearrangements as differences in imaged bands (barcoding) -microarrays can detect very small deletions and duplications that are too small to be identified by barcoding -DNA sequencing and PCR amplification can locate rearrangements down to the level of base pairs.

trisomic

an individual having a single additional chromosome -create a genetic imbalance that is usually deleterious to the organism

monosomic

an individual lacking one chromosome -create a genetic imbalance that is usually deleterious to the organism

deletion heterozygote

an organism that can survive with a chromosome deleted for more than a few genes because its homologous chromosome is normal and has all the missing genes. even though all the genes are present in at least one copy, deletion heterozygotes can have mutant phenotypes for several reasons such as haploinsufficiency (half of the normal gene dosage (# of times a given gene is present in the genome) does not produce enough protein product for a normal phenotype. -very large deletions that include many genes (half or more of a chromosome arm) are usually lethal even in heterozygotes bc of the accumulated smaller effects of halving the dosage of many genes. -another reason why heterozygosity for a deletion can be harmful is that cells become vulnerable to mutations that inactivate the one remaining copy of a gene.

deletion loop

an unpaired bulge of the normal chromosome that corresponds to the area deleted from the other homolog -the progeny of a Del/+ heterozygote will always inherit the markers in a deletion loop as a unit -as a result, these genes cannot be separated by recombination, and the map distances between them, as determined by the phenotypic classes in the progeny of a Del/+ individual, will be zero. -the genetic distance between loci on either side of the deletion will be shorter than expected bc fewer crossovers can occur between them.

telomerase

an unusual enzyme consisting of protein in association with RNA. bc of this mix, it is called a ribonucleoprotein. the RNA portion of the enzyme contains 3' AAUCCC 5' repeats that are complementary to the 5' TTAGGG 3' repeats in telomeres, and they serve as a template for adding new TTAGGG repeats to the end of the telomere. the addition of the new repeats counterbalances the loss of DNA that must occur when linear DNA molecules are copied

transposition

another type of sequence rearrangement with a significant genomic impact. -the movement of small segments of DNA- entities known as transposable elements (TEs)- from one position in the genome to another.

Robertsonian translocation

arise from breaks at or near the centromeres of two acrocentric chromosomes. the reciprocal exchange of parts results in one large metacentric chromosome and one very small chromosome containing few, if any, genes. this tiny chromosome may subsequently be lost from the organism

euchromatin

autoradiography reveals that cells actively expressing genes incorporate radioactive RNA precursors into RNA almost exclusively in regions of euchromatin. indicates that euchromatin contains most of the sites of transcription and thus almost all of the genes.

adjacent-2 segregation pattern

bc of the unusual cruciform pairing configuration in translocated heterozygotes, nondisjunction of homologous centromeres occurs at a low rate. -this nondisjunction causes homologous centromeres N1 and T1 to go to the same spindle pole, while the homologous centromeres T2 and N2 go to the other spindle pole. -resulting genetic imbalances are lethal after fertilization to the zygotes containing them.

crossover suppressors

bc only gametes containing chromosomes that did not recombine within the inversion loop can yield viable progeny, inversions act as crossover suppressors. means that there are few or no recombinants among the viable progeny of an inversion heterozygote.

similarities between the mechanisms by which poly-A-containing and LTR-containing retrotransposons move

both mechanisms begin with transcription of the retrotransposon

duplication

chromosomal rearrangement that alters DNA sequence by adding base pairs

deletion

chromosomal rearrangement that alters DNA sequence by removing base pairs

inversion

chromosomal rearrangement that relocates chromosomal regions without changing the number of base pairs they contain. inversions are half-circle rotations of a chromosomal region -because each DNA strand in a chromosome, even one with an inversion, must run continuously from its 5' to 3' end, the inverted part of the chromosome is not only rotated, but it is also flipped over with respect to the orientations of its two component strands.

reciprocal translocations

chromosomal rearrangement that relocates chromosomal regions without changing the number of base pairs they contain. reciprocal translations happens when two nonhomologous chromosomes exchange parts

constitutive heterochromatin

chromosomal regions that remain condensed in heterochromatin at most times in cells

translocation homozygote

chromosomes separate normally during meiosis 1

chromosome rearrangement

comparisons of the whole-genome sequences from many species have revealed that chromosome rearrangement is a major feature of evolution. for example, each mouse chromosome consists of pieces of several different chromosomes found in humans, and vice versa

DNA microarray

contains allele-specific oligonucleotides for millions of SNP loci. Under the proper conditions, a probe made of fluorescently labeled genomic DNA fragments binds only to complementary ASOs, allowing these loci to be genotyped

nonautonomous elements

defective TEs that require the activity of nondeleted copies of the same TE for movement -in the human genome, all SINEs are nonautonomous elements that can only be mobilized using the proteins encoded by LINEs

pseudolinkage

genes near the translocation breakpoints on the nonhomologous chromosomes participating in a reciprocal translocation exhibit pseudolinkage: they behave as if they are linked

balancer chromosomes

geneticists use crossover suppression to create balancer chromosomes, which contain multiple, overlapping inversions (both pericentric and paracentric), as well as a marker mutation that produces a visible dominant phenotype. geneticists often generate balancer heterozygotes to ensure that a chromosome of normal order, along with any mutations of interest it may carry, is transmitted to the next generation unchanged by recombination. -a parent heterozygous for the balancer and an experimental chromosome will transmit either the balancer or the experimental chromosome, but not a recombinant chromosome, to its surviving progeny.

adjacent-1 segregation pattern

homologous centromeres disjoin so that T1 (T means translocated) and N2 (N means normal) go to one pole while N1 and T2 go to the opposite pole. -each gamete contains a large duplication and a corresponding large deletion, which make them genetically unbalanced. zygotes are usually not viable

types of poly-A-containing retrotransposons

in humans, two major types: -LINEs (long interspersed elements) -SINEs (short interspersed elements) other retrotransposons end in long terminal repeats (LTRs), nucleotide sequences repeated in the same orientation at both ends of the element. this structure is similar to the integrated DNA copies of retroviruses (RNA tumor viruses), suggesting that retroviruses evolved from this kind of retrotransposon, or vice versa. -human LTR-type retrotransposons are in fact called human endogenous retroviruses (HERVs) DNA transposons in other organisms move due to the action of transposase enzyme on the inverted repeats at the ends of the transposon -bc of mutations in the genes they carry or in the end sequences needed for transposition, only a few LINEs and SINEs in the human genome are able to move; the HERVs and DNA transposons in the human genome are immobile relics.

K9-methylated nucleosomes

in the heterochromatin, K9-methylated nucleosomes are bound by HP1 protein, which attracts HMTase enzymes that methylate adjacent nucleosomes and thus spread the inactive "closed" state. -the HP1 protein promotes chromatin compaction into heterochromatin in two ways. first, it self-associates, and this helps to bring adjacent nucleosomes closer together. second, HP1 binds to other proteins, notably including the HMTase enzyme that adds methyl groups to the same K9 amino acid of histone H3. the recruited HMTase can methylate K9 on the histone H3s of the adjacent nucleosomes. this autocatalytic effect provides a partial explanation for the linear spreading of heterochromatin observed in PEV. -methylation of histone tails may either close or open chromatin depending on the particular amino acid methylated. the enzymes that methylate histone tail amino acids are histone methyltransferases (HMTases), and enzymes that reverse histone methylation are called histone demethylases

centromeres in yeast

in yeast, the centromeric DNA is roughly 120 nucleotides long consisting of two highly conserved DNA sequences of 10-15 bp each separated by approximately 90 bp of AT-rich DNA

aneuploids

individuals whose chromosome number is not an exact multiple of the haploid number (n) for the species -autosomal aneuploidy is usually lethal due to genetic imbalance -sex chromosome aneuploidy is usually well tolerated bc only one X chromosome remains active and because the Y chromosome has few genes.

DNA fingerprint

is unique to any one individual, excepting identical twins. assessed using the genotype for 13 unlinked, polymorphic SSR loci

inversion loop

most people with an inversion chromosome are in fact inversion heterozygotes who inherited the inversion chromosome from only one parent. in these individuals, when the chromosome carrying the inversion pairs with its homolog at meiosis, formation of an inversion loop allows the tightest possible alignment of homologous regions. in an inversion loop, one chromosomal region rotates to conform to the similar region in the other homolog. crossing over within an inversion loop produces aberrant recombinant chromatids whether the inversion is pericentric or paracentric.

autonomous elements

nondeleted copies that can move by themselves -the number of fully autonomous elements is small; scientists estimate that a diploid human genome has on average only 80-100 autonomous LINEs -almost all of the 3 million LINE and SINE insertion points are the same in all people, while only about 8000 have mobilized during the course of human history, as evidenced by differing insertion points in different individuals

kinetochores

one of the important ways in which centromeres contribute to proper chromosome segregation is through the elaboration of kinetochores: specialized structures composed of DNA and proteins that are the sites at which chromosomes attach to the spindle fibers. -kinetochores in higher eukaryotes attach to many spindle microtubules -the kinetochore-forming DNA has a different chromatin structure and different higher-order packaging than other chromosomal regions. in this specialized chromatin, the normal histone H3 protein has been replaced by a histone variant called CENP-A in the nucleosome core. the CENP-A protein is very similar to histone H3 in its C-terminal region, but different in its N-terminal portion. nucleosomes with this histone variant act as scaffolds to allow the assembly of many other proteins into kinetochores. -some of these proteins govern kinetochore assembly, some bind microtubules, some are motors that move the chromosomes along the spindle, and some act in a checkpoint that makes sure sister chromatids (mitosis, meiosis II) or homologous chromosomes (meiosis I) do not separate before all the chromosomes are properly attached to spindle fibers

chromosomal rearrangements

one type of event that reshapes genomes by reorganizing the DNA sequences within one or more chromosomes. may effect gene activity or gene transmission by altering the position, order, or number of genes in a cell. such alterations often, but not always, lead to a genetic imbalance that is harmful to the organism or its progeny -chromosomal breakage and subsequent DNA repair can result in all classes of chromosomal rearrangements -aberrant crossing over at repeated sequences can also lead to rearrangements

changes in chromosome number

one type of event that reshapes genomes: involving losses or gains of entire chromosomes or sets of chromosomes. may effect gene activity or gene transmission by altering the position, order, or number of genes in a cell. such alterations often, but not always, lead to a genetic imbalance that is harmful to the organism or its progeny

inversions that exclude the centromere are ___

paracentric -if the inversion if paracentric and a single crossover occurs within the inversion loop, the recombinant chromatids will be imbalanced not only in gene dosage but also in centromere number. -one crossover product will be an acentric fragment lacking a centromere, whereas the reciprocal crossover product will be a dicentric chromatid with two centromeres. -during meiosis, the loss of the acentric fragment and breakage of the dicentric chromatid results in genetically unbalanced gametes, which at fertilization will produce lethally unbalanced zygotes that cannot develop -no recombinant progeny resulting from a crossover in a paracentric inversion loop survive.

inversions that include the centromere are ___

pericentric -if the inversion is pericentric and a single crossover occurs within the inversion loop, each recombinant chromatid will have a single centromere but will carry a duplication of one region and a deletion of a different region -gametes carrying these recombinant chromatids will have an abnormal dosage of some genes. after fertilization, zygotes created by the union of these abnormal gametes with normal gametes are likely to die because of genetic imbalance

SINES

poly-A type retrotransposon derived from pol III transcripts (such as tRNAs) that rely on the LINE-encoded proteins to move after transcription by pol III -structure contains basically only the poly-A tail -length is less than 0.3 kb -in humans, there are 2 million and make up 13% of the human genome

LINES

poly-A type retrotransposon that encodes an RNA-binding protein and reverse transcriptase (the ORF1 and pol genes) that enable their mobilization after pol II transcription. -structure shows the ORF1 gene, pol gene, and poly A tail -length is 6-8 kb -in humans, there are 1 million and make up 20% of the genome fraction

condensins

protein complexes that help condense interphase chromosomes into metaphase chromosomes

allele specific oligonucleotides (ASO)

short 20- to 40-base long oligonucleotides that will hybridize under the right conditions to only one of the two alleles at a SNP locus

replication unit (replicon)

the DNA running both ways from one origin of replication to the endpoints, where it merges with DNA from adjoining replication forks

nucleic acid hybridization

the ability of complementary single strands of DNA or RNA to come together to form double-stranded molecules. the basis for many techniques in molecular biology

nontandem (dispersed) duplications

the copies of the region are not adjacent to each other and may lie far apart on the same chromosome or on different chromosomes.

semisterility

the fertility of most translocation heterozygotes, that is, their capacity for generating viable offspring, is diminished by at least 50%. condition is known as semisterility

core histones

the last four types of histones (H2A, H2B, H3, H4) form the core of the most rudimentary DNA packaging unit--the nucleosome-- and are therefore referred to as ___

satellite DNAs

the more complicated centromeres of higher eukaryotic organisms are contained within blocks of certain repetitive, simple noncoding sequences known as satellite DNAs. many different kinds of satellite DNAs exist, each consisting of short sequences 5-300 bp long, repeated in tandem thousands or millions of times to form large arrays. -the predominant human satellite at centromeres, "alpha satellite", is a noncoding sequence 171 bp in length; it is present in a block of tandem repeats extending over a megabase of DNA in the centromeric region of each chromosome -various human centromeres also contain repetitive sequences unrelated to alpha satellite; these sequences impart heterochromatic characteristics to centromeric regions.

facultative heterochromatin

the phenomenon of position-effect variegation thus reflects the existence of ___: regions of chromosomes (or even whole chromosomes) that are heterochromatic in some cells and euchromatic in other cells of the same organism. -when normally euchromatic genes come into the vicinity of heterochromatin, the heterochromatin can spread into the euchromatic regions, shutting off gene expression in those cells where the heterochromatic "invasion" takes place. in such a situation, the DNA of the gene has not been altered, but the relocation has altered the gene's packaging in some cells -the heterochromatin does not skip over genes as it spreads linearly along the chromosome

shelterin

the protective function of telomeres is due to proteins, different from telomerase, that also bind to the TTAGGG repeats at the very end of a chromosome. these proteins form a complex called shelterin that folds up the telomeres into a structure that shields single-stranded TTAGGG sequences from nucleases (that can progressively DNA inward from the broken ends) and NHEJ enzymes

tandem duplications

the repeated copies lie adjacent to each other, either in the same order or in reverse order

alternative segregation pattern

the two translocated chromosomes go to one pole (T1 and T2), while the two normal chromosomes go to the opposite pole (N1 and N2) -the zygotes formed by the union of these gametes with a normal gamete will be viable

position-effect variegation (PEV)

when a chromosomal rearrangement such as an inversion of a segment of DNA places the gene next to highly compacted heterochromatin near the centromere, the gene's expression may cease. such rearrangements silence gene expression in some cells and not others, producing ____