Epigenetics II: Histone Modifications

Question 1

Position effect variegation in Drosophila is heritable gene silencing by (euchromatin/heterochromatin)

Answer 1

Heterochromatin

Question 2

Antennapedia is the loss of silencing of ________ genes at the wrong time in development

Answer 2

Hox

Question 3

True or false: There is DNA methylation in Drosophila

Answer 3

False

Question 4

What is the fundamental unit of chromatin structure?

Answer 4

Nucleosome

Question 5

H3K4, H3K36 and H3K79 methylation are markers for (on/off) chromatin states

Answer 5

On

Question 6

H3K9 and H3K27 methylation are markers for (on/off) chromatin states

Answer 6

Off

Question 7

What is the function of histone modifications?

Answer 7

Acetylation of lysine side-chains

Question 8

What is the benefit of acetylation of the lysine side-chains?

Answer 8

Neutralizes positive charge and abrogates interaction with DNA

Question 9

Histone acetylation correlates with what events?

Answer 9

Transcriptional activity and dynamic chromatin structure

Question 10

(HDAC/HAT) enzymes are involved in transcriptional activity and (HDAC/HAT) is involved in repression

Answer 10

HAT; HDAC

Question 11

What domains bind to acetylated histones?

Answer 11

Bromodomains

Question 12

Histone lysine methylation is catalyzed by enzymes containing a __________ domain

Answer 12

SET

Question 13

How is histone lysine de-methylated?

Answer 13

Oxidation of methyl lysine by LSD and JMJC enzymes

Question 14

H3K9 methylation characterizes (facultative/constitutive) heterochromatin

Answer 14

Constitutive

Question 15

H3K27 methylation characterizes (facultative/constitutive) heterochromatin

Answer 15

Facultative

Question 16

SUV39H1, SETDB1 and GLP are histone methyltransferases that methylate (H3K9/H3K27)

Answer 16

H3K9

Question 17

EZH1 and EZH2 are histone methyltransferases that methylate (H3K9/H3K27)

Answer 17

H3K27

Question 18

Which heterochromatin protein bind to methylated K9?

Answer 18

HP1

Question 19

Which heterochromatin protein binds to methylated K27?

Answer 19

Polycomb

Question 20

Heterochromatin proteins share a domain. What is the domain?

Answer 20

Chromodomain

Question 21

What technique is used to map histone modifications and chromatin proteins on chromosomes?

Answer 21

ChIP-seq

Question 22

Endoderm specification depends on the (gain/loss) of H3K9me

Answer 22

Gain

Question 23

H3K9me3-dependent (facultative/constitutive) heterochromatin is essential for proper differentiation

Answer 23

Facultative

Question 24

Which family of proteins bind to H3K9me and mediate transcriptional repression?

Answer 24

HP1

Question 25

What properties of HP1 help create heterochromatin "foci" in cells?

Answer 25

Biophysical properties

Question 26

Silencing of which protein requires H3K27 methylation and is a specialized facultative heterochromatin system?

Answer 26

Polycomb

Question 27

In flies, what does a loss of PcG silencing cause?

Answer 27

Developmental transformations

Question 28

In mammals, loss of Polycomb proteins causes what?

Answer 28

Developmental phenotypes like gastrulation defects and neurological defects

Question 29

__________ is a H3K27 methyltransferase complex, with catalytic subunit EZH1/2, AEBP2 and JARID2 that bind to ubiquitylated H2A

Answer 29

PRC2

Question 30

___________ contains Cbx chromodomain proteins that bind to H3K27me mark, also contains RNF2 H2A monoubiquitylation enzyme

Answer 30

PRC1

Question 31

Repression function of H3K27me resides in (PRC1/PRC2)

Answer 31

PRC1

Question 32

Why is the Polycomb system important for oligodendrocyte differentiation?

Answer 32

PRC2 is important to repress signaling pathways that cause cell fate switch and allow myelination by oligodendrocytes Knockout of Eed in OPCs prevent myelination and induce cell fate switch of OPCs to astrocytes

Question 33

Which of the following are ways for DNA/H3K9/HeK27 methyltransferases get to their target genes? a. Interaction with other chromatin factors b. Interaction with site-specific DNA-binding proteins c. Polycomb interaction with coding RNA

Answer 33

a and b

Question 34

How is loop linking DNA methylation to H3K9me formed?

Answer 34

UHRF1 TTD domain binds to H3K9me and UHRF1 SRA domain binds to methyl CpG UHRF1 and DNMT1 interact

Question 35

Methyl-DNA binding proteins like _________ form complexes with HDAC enzymes

Answer 35

MeCP1, MeCP2, MBD