Genetics, Epigenetics

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Genetics, Epigenetics and Dynamic Molecular
Memory
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The Basics Genetics The G,A,T,Cs of
inheritance. Mutations or changes in genotype
may result in changes in phenotype. Epigenetics
Heritable chromatin remodeling. Covalent
modification of DNA or chromatin proteins can be
passed on. Dynamic molecular memory Stable
switching of gene expression which mimics a
mutation in an individual. Relatively stable
covalent modification of DNA or chromatin
proteins.
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GENETICS
Concerns the chemical nature of genes. Central
Dogma DNA-gtRNA-gtProtein
Study of one generation to the next.

• Mutations can change
• DNA -gt protein seq.
• DNA -gt protein folding
• Reg. DNA -gt expression
• Genetic convention
• e.g. CAT -gt CGT
• a4235g DNA change
• H202R coding change

Changes in the genetic makeup of a population
over time and across geographical space.
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Meiosis Simple, but often confusing
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Genetic Animal Models Outbred animals with
diverse genetic make-up, containing multiple
alleles various lab rats Inbred Strain all
animals equal to identical twins (isogenic)
C57BL/6, DBA, most lab mice - homozygous at
ALL alleles Recombinant Inbred Strain inbred
offspring from crosses of two inbred strains
BxD - genetic mix of two strains, but
completely homozygous at ALL alleles Congenic
strain region on one chromosome introgressed
onto different background strain Consomic strain
one whole chromosome is introgressed from one
strain to another Knock out, Knock in a single
gene is removed, completely added or simply
changed - however, keep in mind that since two
strains are used, linked genes fix Transgenic
strain a gene is added in trans i.e. it can
insert anywhere in the genome Line Selectively
bred line of animalssimilar to what we consider
a breed
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Picture worth a thousand words
Consomic strains
Set of genome-wide congenic strains
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Again, BXD RIs --- And, selective breeding
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Gene Expression and Chromatin
Constitutive Heterochromatin chromatin that
usually remains condensed in all
cells Facultative Heterochromatin regions that
are condensed in some cells, and not in
others Euchromatin open, or less condensed DNA
regions
X-inactivation results in Barr bodies with
different X chromosomes shut off in each cell.
Since this is done early in development, a patch
effect is seen.
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Histone modifications alter local chromatin
structure and changes access of transcriptional
machinery to bind DNA
Nucleosome Octet of 2x (H2A, H2B, H3 and H4)
Euchromatin is not simply constitutively active

• Silent Chromatin
• - Hypoacetylation of
• histone H3 and H4
• amino-terminal tails
• - DNAse resistant
• Methylated DNA
• serves as a recruiting
• point for deacetylation
• enzymes
• - H3 can be dynamically
• replaced by varient
• H3.3, an active histone
• protein

Chromosomal regions such as teleomeres that are
tethered to the periphery are silencedbut recent
studies suggest that localization specific
silencing is more complex.
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Eukaryotic regulation of gene expression
Analysis of Bergeson lab microarray data suggests
regional cis-control
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• Epigenetics A change in phenotype that is
  heritable but does not involve DNA mutation.
  (Gottschling. Epigenetics, 2007)
• 1. Position effect variegation (Muller, 1941
  McClintock, 1951 on transposition)
• 2. Trans-control of expression (for example ?
  bacteriophage switching, Ptashne, 2004)
• 3. X Inactivation, Genomic Imprinting
  Facultative Heterochromatin
• 4. Prion disease
• 5. Cytoplasmic Inheritance / Genetic Maternal
  Effect
• microRNA regulation of mRNA content and
  translation of proteins
• __________________________________________________
  ______
• Dynamic Nuclear Organization
• Dynamic DNA modification and the Histone Code

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Position Effect Variegation
The Avy allele map of the A locus and range of
phenotypes in isogenic Avy micea, Avy has an
IAP (subtype II, striped box) inserted in the
pseudoexon 1A of the locus, with the direction of
transcription from the LTRs (arrowhead) opposite
to that of the A promoters. Hair-cycle-specific
non-coding exons (open boxes), coding exons
(filled boxes) and an interrupted inverted repeat
(grey bar arrow) are indicated. The locus is not
shown to scale (100 kb separates the insertion
site and hair-cycle-specific promoters).
Transcription originating in a cryptic promoter
(arrowhead) in the 3' LTR of the IAP in the Avy
allele results in constitutive expression of
agouti in multiple tissues1, 2, 4, 25. b,
Isogenic C57BL/6 Avy/a mice show a continuum of
phenotypes ranging from completely yellow,
through degrees of yellow/agouti mottling, to
completely agouti (termed pseudoagouti because
the mice are isogenic with fully yellow mice and
not genetically agouti). The extent of the yellow
coat colour correlates closely with adult body
weight. Yellow mice have pancellular agouti
expression driven by the inserted IAP. Mottled
mice are mosaics of cells that have or lack
ectopic expression driven by the IAP.
Pseudoagouti mice lack expression from the
cryptic promoter, so that A is regulated by its
hair-cycle promoters, and these mice have the
wild-type coat colour and normal body weight1, 2,
3. Morgan et al., Nature Genetics, 1999.
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Genomic or Parental Specific Imprinting DNA
methylation
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Prion Epigenetics Protein misfolding
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Cytoplasmic Inheritance Genetic Maternal
Effect
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RNA silencing siRNA and microRNA
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Alcohol-induced changes in miRNA expression
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Dynamic Nuclear Organization Chromatin
Mobility within the Nuclear Architecture affects
Gene Expression
Organization of the nucleus
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• Dynamic Molecular Memory
• Covalent DNA modification
• The Histone Code

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• DNA Methylation at CpG dinucleotides
• Used during replication to tag the old strand so
  repair enzymes can fix mutations
• 2. Mechanism of X-inactivation (controlled by
  XIST gene expression, Willard et al., 1993)
• Although always thought be a permanent covalent
  change, new evidence shows that demethylation
  does, in fact, take place making changes plastic.
• Hypomethylation active
• Hypermethylation silent

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DNA Methyltransferases DNMT1 Maintenance of
methylation DNMT2 has weak activity with
unknown function DNMT3A de novo
methylation DNMT3B de novo methylation DNA
Demethylation Understood to be active
removal, but mechanism remains to be elucidated.
(Histone demethylases have been identified.)
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Mismatch Repair
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Covalent Modification of DNA Regulates Memory
Formation Miller and Sweatt, Neuron,
2007
Fear conditioning increases DNA methylation
enzymes.
Proposed molecular mechanism of long-term memory
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Genotype Specific Change in Drinking Associated
with Decrease in Dnmt3b
Bergeson and Blednov preliminary data
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The Histone Code
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Transitions in the Chromatin Template
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Chromatin Modification is Coordinated
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Evidence Age-Specific Epigenetic Regulation by
Binge Alcohol Drinking
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Many Big Questions Remain
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The Future of Epigenetics