Epigenetics

Question 1

H3K4 methylation

Answer 1

H3K4 can be mono/di/trimethylated

associated with permissive active conformation

Question 2

H3K27 Trimethylation

Answer 2

Repressive conformation of chromatin

Question 3

H3K36 trimethylation

Answer 3

actively transcribed coding regions

Question 4

Trithorax

Answer 4

complex responsible for for H3K4 methylation (active)

Catalytic subunit: MLL (methyltransferase)

Question 5

Polycomb complex

Answer 5

Complex responsible for H3K27 methylation (repressive)

Catalytic subunit: Ezh2 (methyltransferase)

Question 6

Demethylases

Answer 6

LSD1 and JumonjiC proteins erase the marks left by polycomb and trithorax

Question 7

Poised chromatin

Answer 7

intermediate between active and silent
Defining marks
-null histone marks
-bivalent chromatin: both active and repressive marks

(these marks apply for noncoding RNA)

Question 8

Histone acetylation

Answer 8

added by HAT removed by HDACs.
Acetylated chromatin classically viewed as active while deacetylation is repressive
may be more complicated than that

Question 9

Canonical histones

Answer 9

H2A, H2B, H3 and H4

Question 10

CpG methylation

Answer 10

Represses transcription when introduced in promoters

Question 11

non CG methylation

Answer 11

non CG methylcytosine is associated with the gene-body region (usually in ES cells)

Question 12

DNMT1

Answer 12

DNA methyltransferase

Question 13

5-hydroxymethylation

Answer 13

5hmC is at transcribed regions, TSS, and some enhancer regions
-Generated by conversion of 5-mC to 5hMC
new epigenetic mechanism crucial for regulating pluripotency and the differentiation of ES cells and HSCs

Question 14

TET proteins

Answer 14

Ten eleven Translocation proteins that convert 5mC to 5 hmC

Question 15

Nucleosome positioning

Answer 15

localization of individual octamers wrt a specific sequence

• active promoters: reduced occupancy
• flanked by two well positioned nucleosomes.
• moved by ATP dependent complexes such as SWI/SNF, ISWI, INO80, SWR, Mi-2/CHD

Question 16

Chromosome looping

Answer 16

can bring together long range regulatory elements

• in cis (on the same chromosome, TH2 LCR)
• in trans (between chromosomes) chr10 IFNg and chr11(IL4)

Question 17

Cis regulatory elements

Answer 17

the DNA elements that control gene epression and constitute an integral part of the gene struction. Contain the binding sites for trans-activating factors serve as the sites of epigenetic modification