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ANAT 381 Experimental Embryology > Epigenetics I: DNA methylation > Flashcards

Epigenetics I: DNA methylation Flashcards

1
Q

What is epigenetics for developmental biologists?

A

Stable propagation of phenotype without a change of genotype

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2
Q

Epigenetics help maintain cellular __________ during development

A

Memory

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3
Q

What is involved in epigenetic effects?

A

Chromatin

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4
Q

High transcription or open chromatin indicate (heterochromatin/euchromatin) and low transcription or closed chromatin indicate (heterochromatin/euchromatin)

A

Euchromatin; heterochromatin

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5
Q

What are components of constitutive heterochromatin?

A

Centromeres, telomeres, retrotransposons

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6
Q

What are components of facultative heterochromatin?

A

Developmental genes, imprinting, inactive X chromosome

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7
Q

What are some cellular mechanisms for altering chromatin structure?

A

Nucleosome movement, assembly and disassembly, large-scale movement of chromatin in the nucleus, covalent modification of chromatin components

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8
Q

True or false: 5-methylcytosine is present in the DNA of all vertebrates and flowering plants, some invertebrates, protists and bacteria

A

True

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9
Q

5-mC is a critical component of the _______ state (heterochromatin)

A

Off

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10
Q

Where is DNA methylation in the genome?

A

CpGs

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11
Q

Most CpGs in the mammalian genome are (methylated/unmethylated)

A

Methylated

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12
Q

Where do a large proportion (40%) of methylated CpGs reside?

A

Retrotransposons

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13
Q

Transcription of retrotransposons by RNA polymerase II leads to what events?

A

Aberrant recombination, insertional mutagenesis, antisense transcription, mobilization

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14
Q

What percentage of promoters of human genes contain CpG islands?

A

70%

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15
Q

CpGs in CGIs are almost always (methylated/unmethylated), at both active and inactive promoters

A

Unmethylated

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16
Q

Rare CGI methylation is strongly correlated with what event?

A

Repression of transcription

17
Q

What type of CGI is commonly methylated?

A

ICRs that control imprinted genes

18
Q

What is methylation at shores associated with?

A

Whether gene is on or off

19
Q

High methylation at shores means (high/low) expression and low methylation at shores means (high/low) expression

A

Low; high

20
Q

What are the regulatory DNA elements that can act at large genomic distances and that are the binding sites for transcription factors?

A

Enhancers

21
Q

High methylation is _____________ with transcription factor binding and enhancer activity

A

Anti-correlated

22
Q

What is the mechanism of repression by DNA methylation?

A

Methyl-DNA binding proteins function in combination with histone modifications to repress transcription and block factor access to DNA

23
Q

What is a technique used to detect CpG methylation?

A

Bisulfite treatment

24
Q

What does bisulfite treatment involve?

A

Treatment of DNA with sodium bisulfite converts unmethylated cytosine to uracil through deamination
Methyl-cytosine is not affected

25
Q

What is the use of bisulfite sequencing?

A

Uracil is converted to thymidine
Able to distinguish methylated and unmethylated cytosines in the genome

26
Q

Which DNA methyltransferase is used for the following
a. Maintenance (inheritance)
b. De novo (establishment of methylation)
c. Germline-specific, targeting function

A

a. DNMT1
b. DNMT3A/B
c. DNMT3L

27
Q

Where does DNMT1 localize?

A

Sites of DNA replication in S phase

28
Q

Where is DNMT3B the major de novo methyltransferase?

A

Embryo

29
Q

What is the role of DNMT3A?

A

Germline development and somatic tissues

30
Q

Which domains of DNMT3A/B bind to chromatin?

A

ADD, PWWP

31
Q

Identify the DNMT mutant phenotype
a. Chromosome stability
b. Loss of imprinting
c. Reanimation of retrotransposons

A

b and c

32
Q

If progenitor cells do not self-renew, what happens to DNMT1?

A

Loss of DNMT1

33
Q

What experiment was done to observe the role of DNMT1 in the renewal of progenitors?

A

WT progenitors and DNMT1 KO progenitors are introduced into an in vivo skin regeneration assay
WT progenitors restore graft, but KO DNMT1 do not
DNMT1 KO progenitors show increased expression of differentiation genes

34
Q

Genes associated with skin cell differentiation are (methylated/unmethylated) in progenitors but (methylated/unmethylated) in differentiated cells

A

Methylated; unmethylated

35
Q

How is DNA de-methylated?

A

Oxidation of 5-mC by TET enzymes
Oxidized 5-mC removed passively by replication or actively removed by DNA repair enzymes

ANAT 381 Experimental Embryology (24 decks)

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