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01 Cell > 2.19 Epigenetics > Flashcards

2.19 Epigenetics Flashcards

1
Q

Set of all the RNAs (both coding and noncoding) produced by a cell or a population of cells

A

Transcriptome

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2
Q

Set of all the proteins produced by the cell at a particular point in time under certain environmental conditions

A

Proteome

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3
Q

True or false

Less nurtured rats had multiple epigenetic marks that silenced these genes

A

True

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4
Q

True or false

Nurtured rats handled stress better because nothing was restricting or silencing the activity of these genes

A

True

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5
Q

Study of changes in gene expression that are stable over rounds of cell division, and sometimes between generations, but do not involve change in the underlying DNA sequence of the organism

A

Epigenetics

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6
Q

Rearranging misplaced tags/markers

A

Epigenetic therapy

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7
Q

Control of gene expression

A

DNA methylation
Histone tail modification
Different types of RNAs

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8
Q

Angelman Syndrome: __ gene deletion

A

Maternal

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9
Q

Prader-Willi Syndrome: ___ gene deletion

A

Paternal

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10
Q

True or false

Epigenetics can have transgenerational effects

A

True

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11
Q

Analyzing patterns of famine and other information in the village archives, it was found that the effects of famine are still evident in the people almost a century later despite not having experienced famine themselves

A

Overkalix study

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12
Q

Some environmental exposure in one generation having effects on future generation

A

Transgenerational effect

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13
Q

True or false

Epigenetic changes accumulate over time

A

True

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14
Q

Older twins have more (red/yellow) in their DNA than the younger twins

A

Red

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15
Q

Happens when two active X chromosomes interact but the other is silenced

A

X inactivation

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16
Q

Allows males and females to have the same dose of genes on the X chromosome even though females have to X’s and males have only one

A

X inactivation

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17
Q

Inactive X chromosome shows DNA methylation of ___

A

CpG islands

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18
Q

Inactivated X chromosome packaged as heterochromatin

A

Barr bodies

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19
Q

XX females have __ Barr body/ies

A

1

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20
Q

XXX females have __ Barr body/ies

A

2

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21
Q

Dispersed, beads on a string, with active histone tail molecules that tag DNA

A

Active chromosomes (Euchromatin)

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22
Q

These are open and accessible to transcription factors and other proteins
Genes are turned ON

A

Active chromosomes

Euchromatin

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23
Q

Tightly bound and condensed, with inactive histone tail modifications

A

Inactive chromosome (Heterochromatin)

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24
Q

Structural proteins that zip the DNA up
DNA is methylated
Less accessible for transcription and therefore silenced
Genes are turned OFF

A

Heterochromatin

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25
Q

The inactive X chromosome in a female somatic cell, rendered inactive in a process called __

A

Lyonization

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26
Q

States that in cells with multiple X chromosomes, all but one is inactivated during mammalian embryogenesis.

A

Lyon Hypothesis

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27
Q

Mechanisms for epigenetic control

A

DNA methylation
Histone Modification
Other regulatory mRNAs

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28
Q

Methylated DNA = gene (silencing/expression)

A

Silencing

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29
Q

Unmethylated DNA = gene (silencing/expression)

A

Expression

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30
Q

Used to maintain genomic stability

A

DNA methylation

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31
Q

Intergenic regions and repetitive elements are usually methylated because these are correlated with jumping genes called __

A

Transposons

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32
Q

DNA methylation usually occurs at ___ turning it into ___

A

Cytosine;

5-methylcytosine (mC/5mC)

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33
Q

A sequence often near promoters of genes where methylation usually occurs

A

CpG Islands

34
Q

True or false

CpG islands are usually methylated

A

False

They are protected from methylation to allow for expression

35
Q

CpG islands are usually site for methylation due to it being ___

A

Symmetrical

36
Q

Can maintain the methylation state after replication by using the hemimethylated DNA as a substrate, and then methylating the other strand accordingly

A

DNMT1

37
Q

Proteins that bind CpG islands are called ___

A

Methylated CpG binding proteins or MeCPs

38
Q

Have a transcriptional repression domain

Recruit other factors that condense the chromatin

A

Methylated CpG binding proteins

39
Q

Mediated by methylation to render gene inactive

A

Imprinting

40
Q

Marking genes as paternal or maternal in origin, in other words, parent-specific gene activation

A

Genomic imprinting

41
Q

Occurs when there is a deletion in the 15q11-q13 region of the paternal chromosome 15

A

Prader Willi syndrome

42
Q

Occurs when there is a deletion in the 15q11-q13 region of the maternal chromosome 15

A

Angelman syndrome

43
Q

Gene involved in Angelman syndrome

A

UBE3A

44
Q

Gene involved in Prader-Willi syndrome

A

SNRPN

45
Q

In Angelman syndrome, UBE3A protein is involved in what pathway

A

Ubiquitin pathway

46
Q

In Prader-Willi syndrome, SNRPN gene is involved in what process

A

mRNA splicing

47
Q

Obesity
Hypogonadism
Mild to moderate mental retardation
Hyperphagia

A

Prader-Willi syndrome

48
Q 
Microcephaly
Ataxic gait (uncoordinated muscle movement)
Seizures
Inappropriate laughter
Severe mental retardation
A

Angelman syndrome

49
Q

True or false

Methylation of C in CpG islands affects globin genes in human embryonic blood cells

A

True

50
Q

True or false

The activity of the globin genes correlates directly with the methylation of their promoters

A

False

Correlates indirectly: high globin activity, unmethylated promoter

51
Q

The erythroid-specific LCR for the beta globins is upstream of epsilon on chromosome __

A

11

52
Q

Function as super-enhancers, establishing open chromatin

A

LCRs

53
Q

Methods of demethylation

A

Passive demethylation

Active demethylation

54
Q

Could happen by dilution when DNMT1 fails to maintain methylation marks after replication and cell division

A

Passive demethylation

55
Q

Important for wiping the slate clear during development

A

Active demethylation

56
Q

Active demethylation is done by specific enzymes ___

A

Ten-Eleven Translocation, TET family of enzymes

57
Q

In an active demetylation, hydroxymethylcytosine is a likely ___ and is ___

A

intermediate; regulatory

58
Q

The bisulphite sequencing cannot distinguish __ and __

A

mC and hmC

59
Q

Distinguish between mC and hmC by running bisuflphite sequencing twice

A

Oxidating bisulfite sequencing

60
Q

Yield information about formylcytosine

A

Resduced Bisulfite sequencing

61
Q

Correlated with gene opening and activation

A

Histone Acetylation

62
Q

Known to occur on lysine residues in the amino terminal tails of histone molecules

A

Acetylation

63
Q

Changes the charge from positive to neutral amide, which decreases the affinity of histone to the DNA

A

Acetylation (of lysine changes)

64
Q

Histone methylation occurs in the amines of __ and __, but there is no change in the charge of the amines

A

Lysine

Arginine

65
Q

Active locus

Around promoter area

A

Methylation of histone 3’s lysine 4 (H3K4me)

66
Q

Inactive locus

Spread over the gene in constitutive heterochromatin (stable inactivation, such as centromeres)

A

Methylation of histone 3’s lysine 9 (H3K9me)

67
Q

Inactive locus

Spread over the gene in facultative heterochromatin

A

Methylation of histone 3’s lysine 27 (H3K27me)

68
Q

Largely unchanged among different cell types
Always condensed and thus essentially inactive
Found in the regions near the chromosal centromere and at chromosomal ends (telomeres)

A

Constitutive heterochromatin

69
Q

Vary among different cell types and tends to be associated with cell type
At times condensed, but at other times it is actively transcribed and thus appears as euchromatin

A

Facultative heterochromatin

70
Q

True or false

Histone modification is stable through rounds of cell division

A

False

Unlike DNA methylation, it does not seem to be as stable

71
Q

DNA methylation tends to ___; Histone methylation tends to ___

A

Silence genes;

Activate or inactivate genes

72
Q

lncRNAs

A

Long noncoding RNAs

73
Q

Have greater sequence specificity due to length
During trnascription, ther are attached or close to their gene of origin
May serve as guide or scaffold for attaching histone modifying enzymes

A

lncRNAs

74
Q

Part of machinery that leads to silencing of one of X chromosomes in females
17-kb, spliced polyadenylated

A

Xist RNA

75
Q

Expressed from one of the X chromosomes, coats it, and leads to silencing of the other X chromosome

A

Xist RNA

76
Q

GAL gene’s expression by RNA polymerase II may be suppressed by:

A

lncRNA transcription on the other side

lncRNA association with hsitones to prevents its modifications to open the DNA

77
Q

Some sort of immune system (anti-transposon, anti-virus) in mammalians

A

PIWI-interacting RNAs (piRNAs)

78
Q

Regulatory RNA which forms a complex with PIWI proteins that can be imported to the nucleus to methylate transposone genes and silence them

A

piRNAs

79
Q

True or false

piRNAs can also direct DNA methylation at sites other than transposable elements

A

True

80
Q

Proportion of individuals carrying a particular variant of a gene

A

Penetrance

81
Q

When not all carriers of a certain dominant allele in a population end up expressing the trait

A

Incomplete penetrance

01 Cell (22 decks)

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