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BMS > Epigenetics > Flashcards

Epigenetics Flashcards

1
Q

Epigenetics

A

Heritable changes in gene function that occur without a change in the DNA sequence

Can be inherited but not DNA changes; can change with different environment

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2
Q

3 modifications of the genome

A

1) DNA methylation
2) histones modification
3) non-coding RNA

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3
Q

DNA methylation: lack of methylation means….

A

Transcription is active

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4
Q

DNA methylation: if methylated….

A

Transcription OFF

Reader recognizes methyl group, enhance blocking of the gene

CpG islands thought out genome, most are methylated

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5
Q

Epigenetics phenomena are characterized by chemical modifications to __ or ___

A

DNA or histones

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6
Q

DNA methylation typically occurs at ____

A

Cytosine bases of DNA, within CpG dinucleotides

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7
Q

CpG islands are associated with

A

5’ regulatory regions of almost al housekeeping genes and 1/2 of almost all housekeeping genes

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8
Q

What happens when promoter CpG islands are methylated

A

Associated genes tend to be transcriptionally inactive

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9
Q

_____ process for maternal demethylation

______ for paternal demethylation

A

Passive for maternal

Active for paternal

As form zygote, everything will be demethylated
Father is actively demethylated in 1-2 division cycles; mother is passively demeythylated until blastocyst (dilution)

*blastocyst –> embryo, maintaining CpG methylation

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10
Q

DNA methylation during mammalian development

A

Wave of demethylation during cleavage, genome-wide methylation after implantation

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11
Q

Extent of methylation in genome of gastrulating embryo is high owing to _____

A

De novo methylation
*tends to decrease in specific tissues during differentiation

*de novo methylation rarely occurs after gastrulation; seen frequently in cancer though

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12
Q

What does dMTase activity do?

A

Demethylase

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13
Q

What does DNA methyl transferase do?

A

De novo methylation

  • need to maintain methylation pattern of cells
  • as replication proceeds, DNAP does not add methyl group on daughter strand; gotta do DNMT maintenance
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14
Q

Transcription factor binding to methylated DNA sequences ____regulates transcriptional output

A

Negatively

TF binds to methylated –> no transcription

DNA sequence regulates TF binding (genetic and fixed)
DNA methylation regulates TF binding (Epigenetic and dynamic)

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15
Q

2 roles of DNA methylation in mammals

A

1) regulation of gene expression
- tissue specific transcription, twin studies, MeCP2: Rett Syndrome

2) Genomic Imprinting

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16
Q

DNA methylation and gene expression twin studies

A

Twins can have Epigenetic tags in different places as they age;

Ex: 50 yr olds have more different Epigenetic tags; rheumatoid arthritis and breast cancer more affected by Epigenetic changes (due to environmental influence) more so than other stuff

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17
Q

Rett Syndrome

A

Autism spectrum disorder with mono genie origin
-progressive neurological developmental disorder
-one of the most common causes of mental retardation in females (1 in 15k females)
-X linked dominant
-period of apparent normalcy: 6-18mos
Life expectancy= 40 years

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18
Q

Mutation in Rett Syndrome

A

MECP2 (CpG binding protein)

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19
Q

MECP2 binds to….

A

Methylated DNA & represses transcription from methylated gene promoters

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20
Q

MECP2 is most abundantly expressed in the

A

Brain

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21
Q

Loss of function of MECP2 in differentiated post-mitotic neurons results in innapropriate_____

A

Over expression of genes with potentially damaging effects during central nervous system maturation

22
Q

Imprinted genes are expressed how?

A

Preferentially or completely from only one allele (paternal or maternal) depending on the specific imprinted gene under consideration

23
Q

Genomic imprinting is the

A

Unequal expression of the maternal and paternal alleles of a gene

24
Q

Do Epigenetic tags on imprinted genes stay put for life of organism? Exception?

A

YES; but they are reset during egg and sperm formation

If came from mother, will remain maternal; same with dad

25
Q

What happens to imprints in sperm?

A

Erased and rewritten with the paternal pattern, even with the genes that came from mom

26
Q

What happens to imprints in eggs?

A

Erased and rewritten with the maternal imprint, even the genes that came from dad

27
Q

If the allele inherited from the father is imprinted it is thereby ___ and only the allele from the ____ is expressed

A

If the allele inherited from the father is imprinted is is thereby silenced and only the allele from the mother is expressed

28
Q

Which 3 vital roles to imprinted genes play?

A

1) embryonic growth
2) neonatal behavior
3) tissue or developmental stage specific monoallelic expression patterns

29
Q

Prader-Willi Syndrome

A
  • disorder of genomic imprinting
  • mental retardation
  • hyperplasia
  • paternal deletion of SNRPN; maternal allele of SNRPN is imprinted by methylation (inactivated)
  • no SNRPN protein at all
30
Q

Angelman Syndrome

A
  • disorder of genomic imprinting
  • excessive laughter
  • seizures
  • mental retardation
  • maternal deletion (angelman, mothers are angels) (SNRPN, UBE3A)
  • -
31
Q

Histones can be ___modified in their ____ which protrude from nucleosomes core particle

A

Histones can be REVERSIBLY modified in their amino terminal tails

32
Q

How can histones be REVERSIBLY modifieD?

A

Acetylation of lysine; opens zipper, allows for transcription
Phosphorylation of serine
Methylation of lysine and arginine residues (prevents transcription)
Sumoylation

33
Q

What happens when histones methylated and who does this?

A 
Closed chromatin
Heterochromatin
Inactive transcription
Writers: methyltransferases
Erasers: Histones deacetylases (HDACs)
34
Q

What happens when Histones acetylated? Who does this?

A

Compact chromatin
Euchromatin
Active transcription

Writers: Histones acetyltransferases (HATs)
Erases: Demethylase

*acetylation increase transcription form (euchromatin) and inactivate transcription thru methylation

35
Q

N termini of core Histones proteins have many lysine residue that have a very ____ charge; these bind tight with negative DNA

Tight binding with DNA and Histones associated with

A

Gene inactivity

36
Q

Positive lysine charge is neutralized by _____ and interaction with DNA is weakened –> transcription can occur

A

Acetylation

37
Q

Non-COding RNA

A

NcRNA is a functional RNA molecule that is transcribed from DNA but not translated into proteins

MiRNA, siRNA, piRNa, IncRNA

38
Q

Long ncRNAs function in

A

Chromatin remodeling
Transcriptional regulation
Post-transcriptional regulation
Precursors for siRNAs

Ex: X chromosome inactivation (XCI)
-2 lncRNAs (Xist and antisense Tsix, negative regulator of Xist)

39
Q

Xist is a ____ transcribed from Xic of inactive C chromosome

A

LncRNA

40
Q

Xist RNA does what

A

Covers the entire chromosome and. Silences gene expression through Epigenetic modification of Histones and DNA

Xic of inactive X transcribes lncRNA XIst–>covers the entire chromosome and silences gene expression via Epigenetic modification of Histones and DNA

41
Q

What represses Xist and how?

A

Tsix

Both Xist and Tsix produce ncRNA transcripts; Tsix RNA transcript is antisense to Xist

Tsix can bind to the Xist sequence and inhibit its action, preventing X-inactivation
Depends on who produces what? When 2 X”s coming together, exchanging factors which determines who’s making more of what ( hypothesis)

42
Q

How is XIC (X-inactivation center) established?

A

Pre-XIC: both chromosomes have low conc of Xist
Establishment of XIC: one X will make a lot of Tsix —> there will be reduction of Xist in the area around this X chromosome

Therefore, X inactivation is inhibited, and this chromosome will be the active X chromosome

43
Q

Phenotypic plasticity

A

Ability of one genotype to produce more than one phenotype when exposed to different environments

(As the modification of developmental events by environment, or as the ability of an individual organism to alter its phenotype in response to change in environmental conditions

44
Q

What can cause phenotypic plasticity

A

Environmental effects (ex: hunger winter) may involve Epigenetic changes in gene function that get passed down

Adult neuronal plasticity and neurogenic is; changes in chromatin marks & transcriptional networks associated with sustained neuronal activity, mood disorders, addiction

45
Q

Not methylated agouti gene

A

Continuously active, producing mRNA across lifespan

Mouse with yellow fur

Develops obesity and diabetes during adulthood

46
Q

Methylated agouti gene

A

Agouti mRNA made briefly during development

Agouti gene silenced remainder of mouse life

Healthy mouse, brown fur

47
Q

Are fat yellow mice and skinny brown mice genetically identical

A

Yes

Methylation or lack of determines weight and whether prone to disease or not

48
Q

What happened when fat yellow mouse (agouti gene unmethylated and active) had diet supplement during pregnancy and nursing with additional methyl groups?

A

Offspring mostly brown and healthy; agouti gene methylated and silenced

No dietary supplementation? Offspring yellow and unhealthy

49
Q

Bisulfide conversion of DNA

A
  • method to study changes in epigenome
  • bisulfide converts C to U if C is NOT METHYLATED
  • use reverse transcriptase, PCR, DNA sequencing, or methylation specific restriction enzyme digestion to determine methylation status of specific strand

Methylated cytokines don’t react with bisulfide; allows us to determine methylation status of different genes

50
Q

How to detect DNA methylation with methylation sensitive restriction enzymes?

A

Methylation insensitive (MspI) cuts enzyme; methylation sensitive (HpaIIdoes NOT cut DNA where it is methylated !!!

(Both restriction enzymes cut same sequence aka isoschizomer)

Methylation insensitive is insensitive and CUTS

BMS (7 decks)

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