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EXMD 504 > Lecture 6 > Flashcards

Lecture 6 Flashcards

1
Q

true or false: altered patters of gene expresson is a key feature of cancer

A

true

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2
Q

the disruption of epigenetic regulatory mechanisms is…. in cancer

A

prevalent

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3
Q

true or false: we can use altered patters of gene expression to stratify patients

A

true

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4
Q

aberrant gene expression can be driven by what

A

specific genomic/epigenomic alterations

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5
Q

different cell types are programmed to express….. set of genes

A

different

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6
Q

true or fa;se: different cell types are programmed to express different sets og genes but they share the same dn

A

true

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7
Q

The establishment of different cell
lineages and cell differentiation involves
different gene expression programmes
during….

A

developmen

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8
Q

The establishment of different cell
lineages and cell differentiation involves
different gene expression programmes
during development, which do not
depend on the DNA sequence itself, but
instead on …… factors.

A

“epi”-genetic

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9
Q

Epigenetics covers all ….

A

Epigenetics covers all phenomena that
produces heritable changes in genome
function that do not affect the DNA
sequence

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10
Q

The expressiom state of a gene is determined by what

A

-the packaging or the accessibility of its dna in the chromatin
-by the presence of transcription factors and chromatin modifying enzymes

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11
Q

accessibility of chromatin to transcriptional regulation is controlled by what?

A

-modification to the DNA
-modification/rearrangement of nucleosomes

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12
Q

true or false: dna is wrapped in nucleosome

A

true

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13
Q

what are the 2 subunits in each histone?

A

-h2a. h2b
-h3 and h4

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14
Q

true or false, the nucleosome has an S terminus

A

false it has a N terminal tails of the histones protrude out of the nucleosome

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15
Q

what does the pattern of histone modification signify

A

the status of the chromatin (histone code)

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16
Q

true or false: you can change the N terminal tails

A

you can’t change the tails post transitionally

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17
Q

The enzymes regulating the post-translational epigenetic modifications on histones have been categorized as…

A

writers
erasers
readers
movers

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18
Q

what do writers do

A

-add modifications aka analogous to kinases
-ex: histone lysine methyltransferases (KMTs), and histone
acetyltransferases (HATs)

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19
Q

what do erasers do

A

-remove post translational modifications aka like phosphatases
ex:Histone lysine demethylases (KDMs) and histone deacetylases
(HDACs)

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20
Q

what do readers do

A

-are proteins that “read” histone modifications, such as acetylated or methylated residues.
* Bromodomain and chromodomain containing proteins
* Bromodomain recognize the acetylated lysines
* Chromodomain recognize methylated lysines

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21
Q

what di movers do

A

are chromatin-remodeling proteins that move nucleosomes and allow gene transcription.

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22
Q

histones can be replaced by what

A

minor variants

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23
Q

what is the role of H3.3

A

important in transcriptional activation

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24
Q

how do histone variants differ

A

from the canonical histone by just a few am,ino acid

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25
Q

the minor histone variants are synthesized throughout when

A

interphase and are often inserted into previoulsy formed cjromatin by a remodeling complex

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26
Q

true ot false: Epigenetic Modifications Annotate Functional
Elements Across the Genome

`

A

true they annotate non coding elements

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27
Q

what do we use for mapping the epigenome

A

chip seq

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28
Q

what does the chip seq pull down

A

the methyl group

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29
Q

what are the active promoters of h3k4

A

h3k4me2 and me3

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30
Q

what do you use to mapp the genome

A

atac seq

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31
Q

what does atac seq do

A

assay for transposase accessible chromatin using sequencinf

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32
Q

Epigenetic mechanisms act to change the accessibility of chromatin to transcriptional regulation via …..

A

modification to DNA or by modification / rearrangement of nucleosomes (histones).

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33
Q

true or false: global dna methylation patterns vary between different cell types and different stages in devlopment

A

true

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34
Q

what is the main role of dna methylation

A

dna silencing
-Genomic imprinting
* Differential expression of maternally and paternally inherited alleles
* X-chromosome inactivation: Compensation for sex differences in gene dosage
* The suppression of retrotransposon elements.

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35
Q

dna methylayion is limited to ….

A

cytodines and occurs within the contect of the di nucleotide cg

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36
Q

what so dnmt3a and B do

A

are de novo
methyltransferases that they methylate CG
dinucleotides
* The DNMT1 enzyme maintains existing
DNA methylation patterns
-they are writers

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37
Q

what does tet do

A

-TET (ten-eleven translocation) enzymes
are methylcytosine dioxygenases (initiate
demethylation
-tis an eraser

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38
Q

true or false: C→T mutations are rare in human DNA.

A

false: common

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39
Q

what are c to t mutations

A
  • Deamination of cytosine is a very common
    reaction in cells and normally produces uracil
  • Uracil is found in RNA, not DNA.
  • Cells are equipped with uracil DNA glycosylase
    that removes them as part of the base excision
    DNA repair pathway.
40
Q

Deamination 5-methylcytosine produces….

A

thymine

41
Q

DNA methylation is limited to what and occurs when

A

it is lomited to cytosines and occures within the context of the di nucleotide cg

42
Q

what are cpg islands

A
  • have a G + C-rich base composition (65% vs 40% for the bulk genome)
  • high density of the dinucleotide CpG (5–10-fold higher than the bulk genome)
43
Q

how long are cpg islands

A

1kb or less

44
Q

where are usually cpg islands

A

50% of them are located close to known transcriptional start sites
-25% are found in main gene body

45
Q

CGIs associated with transcriptional start sites remain ….. even when the gene is not being transcribed

A

unmethylated

46
Q

why are cpg islands importnat

A

because they represent areas of the genome that have been protected from the mutatong properties of methylation through evolutionary time aka deamination

47
Q

true or false: dna amination changes are observed in cancer

A

i dunno but methylation yes

48
Q

General …..methylation of the
cancer genome

A

hypomethylation ‘

49
Q

focal hypermethylation/silencing of tsg promoters, what is there?

A

CpG island methylator Phenotype (CIMP)

50
Q

direact mutagenesis of …. containinh sequences of deamination

A

5mc

51
Q

Changes in the chromatin structure are dependent of changes ……

A

in DNA methylation, histone modification and the positioning of nucleosomes

52
Q

what are oncogenes

A

dominantly acting cancer genes that resut from an activating mutation in one allele of a cellular proto-concogene

53
Q

oncugenes are often activated by loss or gain of function

A

gain of funstion

54
Q

why are oncogenes over expressed

A

due to gene amplification

55
Q

what is epigenic enhancer hijacking

A

Activated by structural variants that reposition a transcriptionally silenced gene so that it comes under the control of active regulatory elements

56
Q

what are tumor suppressors

A

recessive acting cancer genes in which the inativation of both alleles promotes cell proliferation or inhibits apoptosis
-can be mutations, deletions, dna methylation or combination

56
Q

true or false: a big number of single nucleotide variants are driver mutations

A

false it is a small number

57
Q

single nucleotide variants can driver mutations, are they positively or negatively selected

A

positively because they confer proliferative advantage to cancer cells

58
Q

name one way to detect cancer driver genes

A

you look at the genome of those affected vs not and see which is the most mutated

59
Q

missence vs truncated which is is a driver and a suprssor

A

-missense: driver
-trunctative: suppresive

60
Q

IDH1 mutation is sufficient to establish what

A

the glioma hypermethylator phenotype

61
Q

IDHD1 is involved in which process

A

-the TCA
DH1/IDH2 cancer-associated mutations
are specific missense mutations
producing mutant enzymes that convert
2-oxo-glutarate (produced by the normal
allele) to 2-hydroxyglutarate.

62
Q

what does 2-hydroxyglutarate do

A

2-hydroxyglutarate inhibits multiple
enzymes that depend on 2-oxoglutarate
as a cofactor and work in epigenetic
modification, including certain DNA
demethylases, such as TET2, and various
histone demethylases. That can cause
reprogramming of the cell to make it less
differentiated

63
Q

what are copy number variants useful for

A

to detect cancer, more copy number variants= cancer

64
Q

if there is a gain of copy in someone that has a tumor what does it mean and deletions too

A

-more cpoies= oncogene
-less copies= supressor

65
Q

true or false: tumor genome is not the same as the reference genome

A

true
* Copy number gains can be
incorporated into the Genome
(ie. Tandem duplications)
* However, many high-level
amplifications occur on circular
extrachromosomal DNA
(ecDNA)

66
Q

what does circular ecdna promote

A

accessible chromatin and high oncogene expression

67
Q

true or false: half of human cancer mutations harbor mutations in chromatin related proteins

A

true

68
Q

what do malignat cells exhibit

A
  • Genome-wide alterations in DNA
    methylation
  • Chromatin structure
  • Regulatory element activity
  • Deranged developmental programs
  • a differentiation block or epigenetic reprogramming
69
Q

driver mutations in h3.3 and chromatin remodeling genes are in which canver

A

paediatric glioblastoma

70
Q

what is chondroblastoma and giant cell tumor og bone have for mutatins

A

h3f3a and h3f3b mutation

71
Q

Mutations in histone H3.3 (encoded by H3F3A or H3F3B) commonly occur at three residues: ….

A

K27, K36 and G34.

72
Q

H3.3-K27M and H3.3-K36M mutations are dominant …… and reduce the genome-wide ……. of H3K27 and H3K36, respectively

A

H3.3-K27M and H3.3-K36M mutations are dominant negative and reduce the genome-wide methylation of H3K27 and H3K36, respectively

73
Q

H3.3-G34R and H3.3-G34V mutations reduce the levels of ….. on the same or nearby nucleosomes

A

H3K36me3

74
Q

The …… chromatin Remodeling Complex
is altered across many cancer types

A

h* >20% of all cancers harbour mutations in
SWI/SNF-encoding genes

75
Q

how many genes encoding for the swi/snf family are mutated in cancer

A

9

76
Q

Mutations in specific SWI/SNF genes are enriched in particular cancer types, which suggests …….

A

-differential roles for individual components
-The tumour-suppressor activity is most likely attributable to their roles in facilitating transcription factor function, which is central to cell-fate differentiation.

77
Q

true or false: chromatin remodelers are multi subunit complexes

A

true

78
Q

what do chromatin remodelers use

A

use the energy from atp hydrolysis to reposition, eject, slide ot alter the composition of nucleosome

79
Q

what do chromatin remodelers do

A

allow access to dna binding proteins and the transcriptional machinery to dna in order to facilitate gene expression

80
Q

true or false:swi/snf and pcr complex help eachother

A

nah they probs fuck eachother up

81
Q

Noncoding mutations in regulatory elements can lead to …..

A

the aberrant expression of oncogenes, transcription
factors and chromatin regulators resulting in aberrant gene expression

82
Q

true or false: non coding regulatory elements harbor a larger fraction of somatic mutations

A

true

83
Q

is tert coding or non coding

A

non coding
involved in mutations in human melanoma, glioblastoma, oligodendroglioma

84
Q

recurrent non coding u1 snrna mutations drive what

A

cryptic splicing in shh medulloblastoma

85
Q

true or false: Noncoding enhancers outside of oncogenes ( ie. MYC, MYCN, AR,
KLF5, and EGFR) are always selectively amplified with their respective oncogenes

A

false it is with or eithout
with: myc, mycn
without myc too often just duplicated

86
Q

what can enhancer hijacking events explain

A

aberrant gene expression patterms

87
Q

true or false: tads interact with eachother

A

false they interact with themselves but not eachother

88
Q

explain chromatin 3d thing

A

idsabfyrgaofao

89
Q

enhancer hijacking activated wich family in oncogenes in meduloblastoma

A

GFI1

90
Q

can you duplicate an enhancer in cancer

A

yeah especially in tads, you can delete,

91
Q

…… Duplication is highly recurrent in Group 4 Medulloblastoma

A

SNCAIP

92
Q

true or false, enhanver hijacking events are common

A

true

93
Q

what does ecdna do

A

enables distal dna interactions

94
Q
A

EXMD 504 (12 decks)

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