BIMS 320 TEST 3

Monzygotic twins

"Epigenetic differences arise during the lifetime of monozygotic twins" - Mario Fraga 2005

Constitutive enzymes

- Enzymes continuously produced regardless of chemical makeup of the environment

Transition vs. Transversion

Transition: if a pyrimidine replaces a pyrimidine or a purine replaces a purine Transversion: if a purine replaces a pyrimidine, or vice versa

Mechanisms regulating genomic imprinting

- Differentially Methylated "CpG islands". - Differential active and repressive histone modifications.

Induced mutations

- result from the influence of an extraneous factor, either natural or artificial.

Chapter 15

Gene Mutation, DNA repair, and Transposition

Open vs. Closed configuration of chromatin

Open: - DNA is unmethylated and histones are acetylated - Genes can be transcribed Closed - DNA is methylated at CpG islands - histones are deacetylated - genes can not be transcribed

Regulatory proteins

*indirectly or directly assist RNA polymerase* 1. A domain that recognizes the proper regulatory element . 2. A domain that interacts with RNA polymerase or any of its associated proteins. 3. A domain that interacts with proteins at nearby docking sites. 4. A domain that influences chromatin condensation 5. A domain that senses physiological differences in the cell.

Inducible enzymes

- Bacteria are nutritional opportunists--they "swim" in their environment, and use the compounds that are available instead of making them. - Bacteria adapt to their environment by producing *these certain enzymes* only when specific substrates are present - An abundance of an end product in the environment represses gene expression

Base replacement

- Chemical compounds similar to nucleotides become incorporated into DNA. - Cause mispairing, and incorrect nucleotides to be incorporated during replication. - 5-BU causes GC-->AT or AT-->GC transitions during replication. - 2-AP (2-amino-purine) is an analog of adenine that mispairs with cytosine.

Function of CpG methylation

- Genomic stability - Represses retrotransposons - Formation of heterochromatin --> X chromosome inactivation --> Centromere - Controls transcription

Angelman's Syndrome

- Loss of function of maternal UBE3A - *maternal inheritance of deletion* - 1/10,000-1/20,000 - Severe intellectual disability (IQ 30-50) - Ataxia (loss of full control of body movements) - Seizures - Absent speech

Prader-Willi Syndrome

- Loss of paternal derived HBII-85 snoRNA - *paternal inheritance of deletion* - Feeding difficulties - Failure to thrive - Mild developmental delay - Hypotonia (state of low muscle tone/strength) - Severe obesity

Histone Modifications

- N0terminal region of each histone extends beyond the nucleosome, and amino acids in these tails can be covalently modified in several ways - includes addition of acetyl, methyl and phosphate groups - alter the structure of chromatin, making genes on nucleosomes accessible or inaccessible for transcription - *writers*: proteins that add chemical groups - *readers*: proteins that interpret these modifications - *erasers*: proteins that remove these chemical groups

Base Alteration

- Some mutagens (EMS--ethylmethanesulfonate) alter bases, causing mispairing. - Add alkyl groups to positions on all four bases. - Result in GC-->AT transitions. - Intercalating agents 1. Proflavin 2. Acridine orange 3. ICR compounds. - Cause singlenucleotide-pair insertions or deletions

Gene Regulation

- What allows different types of cells to have different functions even though they all contain the same DNA - Only a fraction of different genes are expressed at a given time during development or at different times in an organism's lifespan. - The differences are caused by differences in cell or tissue-specific gene regulation. Occurs at many levels 1. Adjusting the transcription of DNA into RNA, or translation of RNA into protein. 2. mRNA stability 3. Posttranslational modifications of proteins. *Most regulation occurs at the level of transcription.*

point mutation

- a change of one base pair to another - aka *base substitution* Possible outcomes 1. creation of a new triplet that codes for a different amino acid in the protein product (a *missense mutation*) 2. triplet will be changed to a stop codon, resulting in termination of translation of the protein (a *nonsense mutation*) 3. codon is altered but does not result in change in the amino acid that position in the protein (due to degeneracy of the genetic code) (a *silent mutation*)

Epigenetic trait

- a stable, mitotically and meiotically heritable phenotype that results from changes in the pattern of gene expression without alterations of the DNA sequence

HAT complex

- activator binding recruitment of HAT complex causes histones to be acetylated - *transcriptive activation* by allowing attachment of RNA polymerase II

behavioral mutations

- affect behavior patterns of an organism - ex: mating behavior of fruit fly may be impaired if it cannot beat its wings - harder to observe --> defect may be in flight muscles, nerves leading to them, or the brain

regulatory mutations

- affect regulation of gene expression bc mutation is located in regulatory region

DNA methylation

- aka *CpG methylation* - in mammals, takes place after replication and during cell differentiation - *Methyl group added to the #5 carbon of cytosine located 5' to guanine* - almost exclusively on cytosine bases located adjacent to guanine base (a*CpG dinucleotide*) which are clustered in regions called *CpG islands* but can also occur at non-CpG islands - CpG islands are located in and near promoter sequences adjacent to genes - this is a reaction catalyzed by family of enzymes called DNA methyltransferases (DNMTs) - normal process during development (ex: X chromosome inactivation is associated with DNA methylation of these groups) - abnormal patterns of DNA methylation are associated with specific human diseases, including cancer - *Demethylase* is an enzyme that can demethylate these groups

CpG island

- area of DNA with > 200 bp with GC content > 50% and observed CG ratio > 60%

Reprogramming

- at fertilization, mammalian embryo receives maternal and paternal set of chromosomes - maternal set carries female imprints and paternal set contains male imprints - when gamete formation begins in female germ cells, both maternal and paternal imprints are erased and reprogrammed to a female imprint that is transmitted to the next generation through the eggg - opposite for male germ cells Reprogramming occurs at 2 stages 1. erasure by demethylation and reprogramming by remethylation lay down a male or female-specific imprinting pattern in germ cells of the parent 2. large-scale demethylation occurs in embryo sometime before 16-cell stage of development. After implantation, differential genomic remethylation recalibrates which maternal alleles and which paternal alleles will be inactivated *remember, imprinted alleles remain transcriptionally silent in all cells, while genes silenced by epigenetic methylation can be reactivated by external signals*

Maternal behavior

- can have effect on epigenome - ex: mothers that lick and groom and use arch-back nursing in rats saw offspring with differences in CpG methylation, histone acetylation, etc.

Epigenetic Modifications

- covalent modifications imparted onto either DNA or histone proteins. - They mask or expose regulatory elements (enhancers/silencers) and promoters

biochemical mutations

- do not always affect morphological characters, but they affect the function of proteins that can affect the well-being and survival of affected individuals - ex: sickle-cell anemia, hemophilia

conditional mutations

- effect on organism depends on environment in which organism finds itself - ex: temp-sensitive mutations

Maternal nutrition

- effects the epigenome - "Transposable elements: targets for early nutritional effects on epigenetic gene regulation." - RA Waterland 2003

Spontaneous mutations

- happen naturally and randomly and are usually linked to normal biological or chemical processes in the organism.

Epigenetics in imprinting

- imprinting is an epigenetically regulated process in which genes are expressed in a parent-of-origin pattern; that is, certain genes show expression of only the maternal allele or the paternal allele - results in the differential allelic expression of certain genes. This leads to the expression of one allele and repression of the other allele. - caused by differential methylation of CpG-rich regions and methylation of promoter sequences that produce allele-specific imprinting and subsequent gene silencing - once a gene has been impritned, it remains transcriptionally silent during embryogenesis and development - most imprinted genes direct aspects of growth during prenatal development - having only one functional allele makes impritned genes highly susceptible to deleterious effects of mutations

nutritional mutation

- in bacteria and fungi, results in loss of ability to synthesize an amino acid or vitamin

Recessive mutation

- most loss-of-function mutations - results in wild-type phenotype when present in a diploid organism and the other allele is wild type - in this case, the presence of less than 100 percent of the gene product is sufficient to bring about the wild-type phenotype

lethal mutation

- mutation that adversely affects a gene product that is essential tot he survival of the organism

neutral mutations

- mutation that can occur etiher in a protein-coding region or in any part of the genome, and its effect on the genetic fitness of the organism is negligible.

Epimutations

- mutations in imprinted genes can arise by dysfunctional epigenetic changes

gene mutations

- mutations occurring primarily in the base-pair sequence of DNA within individual genes - different than mutations in large regions of chromosomes (chromosomal mutations) - cell can defend itself from such mutations using various mechanisms of DNA repair - the extent to which a mutation changes the characteristics of an organism depends on which type of cell suffers the mutation and degree to which the mutation alters the function of a gene product or a gene-regulatory region

null mutations

- mutations that result in complete loss of function

Mutagens

- natural or artificial agents that induce mutations. - Different mutagens have different mutational specificities for types and sites. 1. Base replacement: changes the base itself. 2. Base alteration: causes the base to mispair with another base. 3. Base damage: makes the base unable to pair

Somatic mutations

- occur in any cell except germ cells and are not heritable.

Germ-line mutaitons

- occur in gametes and are inherited.

loss-of-function mutation

- one that reduces or eleminates the function of the gene product - any type of mutation, from a point mutation to deletion of the entire gene, may lead to loss of functions

Epigenome

- refers to pattern of epigenetic modifications present in a cell at a given time. - cell-type specific and changes throughout the life cycle in response to environmental cues - an organism has one genome, which can be modified in diverse cell types at different times to produce many epigenomes - can be transmitted to daughter cells by mitosis and future generations by meiosis

mutation hot spots

- some DNA sequences that appear to be highly susceptible to mutation

Dominant mutation

- some loss-of-function mutations - results in a mutant phenotype in a diploid organism, even when the wild-type allele is also present - Dominant mutations can have 2 different types of effects 1. Haploinsuffiency (occurs when single wild-type copy of gene does not produce enough gene product to bring about a wild-type phenotype) 2. Dominant gain-of-function mutation (results in gene product with enhanced, negative, or new functions)

Epigenetics

- study of the ways in which chemical modifications to DNA and histones after cell- and tissue-specific patterns of gene expression - emerging field of Epigenetics is providing us with molecular basis for understanding how heritable changes other than those in DNA sequence can influence phenotypic variation - (ex: monozygotic twins that have identical genotypes but often have different phenotypes)

Histone code

- sum of complex patterns and interactions of histone modifications that alter chromatin organization and gene expression - combinations of these changes allow differentiated cells to carry out cell-specific patterns of gene transcription and to respond to external signals that modify these patterns without any changes in DNA sequence

frameshift mutation

- the *insertion* or *deletion* of a nucleotide causes all the subsequent three-letter codons to be changed - will occur when any number of bases are added or deleted, except in multiples of 3, which would reestablish the initial frame of reading

mutation rate

- the likelihood that a gene will undergo a mutation in a single generation or in forming a single gamete

visible mutations

- those that affect morphological trait and therefore are most easily observed -

HDAC complex

- with repressor and HDAC complex, histones are deacetylated - *transcriptive repression*

3 major epigenetic mechanisms

1. reversible modification of DNA by addition or removal of methyl groups 2. Chromatin remodeling by addition or removal of chemical groups to histone proteins 3. regulation of gene expression by non-coding RNA molecules

DMR

Differentially Methylated Region - CpG island - Promoter --> Sense or antisense (*?*) - Regulates imprinting of one gene - Methylated on only one parental chromosome (differential) - Typically represses the expression of the methylated allele

Chapter 16

Regulation of Gene Expression in Prokaryotes