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MCT > Epigenetics > Flashcards

Epigenetics Flashcards

1
Q

Wet-lab method to determine precise nucleosome positioning and phasing

A

MNase-seq and MNase-chip

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2
Q

Histones have ________ charged N-temrinal tails that interact with nearby nucleosomal DNA. This allows for higher order packing.

A

Positively

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3
Q

What affect does histone acetylation have on DNA?

A

Opens it up
(-) negates (+) tail charges
Promotes tc

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4
Q

What affect does histone methylation have on DNA?

A

Depends on where methylation occurs
K4: activated tc
K9: repressed tc

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5
Q

Histone modifications have _____ peaks around promoters, and _____ peaks throughout gene.

A

Sharp (promoters)

Broad (throughout gene)

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6
Q

Block deacetylation

Promote tc of tumor suppressor genes

A

HDAC inhibitors

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7
Q

2 pathways to active tc through modifying histones / nucleosomes

A

HATs (histone acetylases)

ATP dependent remodeling complex (remodels nucleosomes)

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8
Q

Cytosine ___________ at promoters leads to silencing of nearby genes.

A

methylation

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9
Q

What are some roles of DNA methylation?

A

Tc silencing of promoters
Protecting genome from transposition repetitive elements and viral gene expression
Genomic imprinting
X inactivation
Tissue and developmental specific gene expression
Blocking binding to some TFs

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10
Q

Responsible for de novo methylation (early in development)

A

Dnmt3a

Dnmt3b

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11
Q

Responsible for maintenance methylation after DNA replication

A

Dnmt1

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12
Q

Some genes are expressed only from the maternal genome or only from the paternal genome
Maintained by DNA methylation

A

Genomic imprinting

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13
Q

DNA methylation writers

A

DNA methyl transferases (DNMT)
Dnmt1
Dnmt3a
Dnmt3b

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14
Q

DNA methylation erasers

A

Tet family

passive erasing during cell division

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15
Q

DNA methylation readers

A

Methyl binding domain proteins

MeCP2

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16
Q

Identifies histone modification and protein-DNA binding sites

Cross link proteins to DNA, sonicate to shear, immunoprecipitate with Ab to TF/histone/histone modification, reverse cross links and sequence

A

ChIP

Chromatin Immunoprecipitation

17
Q

Active gene regulatory elements (promoters, enhancers, silencers, insulators, LCR, meiotic recombination hotspots) are DNase ___________

A

hypersensitive

tightly wrapped DNA more resistant to DNase

18
Q

Coding sequence mutation that disrupts chromatin regulator

MECP2 causes:

A

Rett syndrome

19
Q

Coding sequence mutation that disrupts chromatin regulator

CHD7 causes:

A

CHARGE syndrome

20
Q

Coding sequence mutation that disrupts chromatin regulator

H3F3A/HIST1H3B causes:

A

DIPG

21
Q

Noncoding mutations that impair gene regulation IGF2/H19 causes:

A

Beckwith-Wiedemann syndrome

22
Q

Noncoding mutations that impair gene regulation CACNA1C corresponds to:

A

Schizophrenia

23
Q

Loss impairs synaptic development in brain
Regulates long neuronal genes that are labeled by mCA (neurons accumulate on-CpG methlyatlion after birth)
Mutation leads to Rhett syndrome on X chromosome (affects mostly girls - mosaics, lethal in boys)
(neuron selectivity)

A

MeCP2

24
Q

Chromodomain helicase that remodels nucleosome architecture at regulatory elements
Mutation affects neural crest cell differentiation and migration, which leads to CHARGE
(phenotype variability)

A

CHD7

25
Q

Mutations in these histone genes lead to DIPG (diffuse intrinsic pontine glioma)
Histone amino acid change (often from lys27 to met)
Mutations leads to global depression of cancer promoting genes
(regional specificity)

A

H3F3A

HIST1H3B

26
Q

Impaired methylation of imprinting control region regions (for IGF2/H19 domains) on chromosome 11p15.5 is associated with:

A

Beckwith-Wiedemann Syndrome

27
Q

Schizophrenia associated SNPs in ___________ enhancers impair tc of the calcium channel
(mechanistic discovery)

A

CACNA1C

28
Q

Maternal care in mice influxes later ________ response via methylation of the glucocorticoid receptor gene
Nr3c1 expression
(vulnerability and resilience)

A

stress

29
Q

Feeding agouti mice dietary supplements results in _________ of the Avy transposon, reversing coat color
(you are what you eat)

A

methylation

MCT (13 decks)

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