Histones

Question 1

Describe the general compaction stages of chromatin

Answer 1

1. DNA (2nm diameter)
2. Nucleosomes with DNA wrapped around them (11nm)
3. Chromatin fibers, aka coiled nucleosomes (30nm)
4. 300nm
5. 700nm
6. Mitotic chromosome (1400nm shorter length)

Question 2

Describe the nucleosome structure

Answer 2

H3H4 tetramer + 2 * H2AH2B dimers

Question 3

What are the relevant PTMs for histones

Answer 3

Me, Ac, P, Ub

Question 4

How many methylations can you have on a Lysine?

Answer 4

3

Question 5

What amino acid is most often acetylated?

Answer 5

Lysine

Question 6

What aminoacids can be phosphorylated?

Answer 6

Ser(most common), Thr, Tyr

Question 7

What amino acids are methylated

Answer 7

Lys(3), Arg(2)

(also Gln, His, Asn, Cys, Glu)

Question 8

Euchromatin histone PTMs

Answer 8

H3K4me
H3K36me
H3K9ac
H4K16ac

Question 9

Constituitive hetero histone PTMs

Answer 9

H3K9me

Question 10

Facultative hetero histone PTMs

Answer 10

H3K27me
H2AK119Ub

Question 11

Chromatin domains

Answer 11

Enhancer
Promotor
Gene body
Insulator
Gene cluster
Repeat

Question 12

H3K4me3 vs H3K4me1

Answer 12

active promotor vs enhancer

Question 13

what HPTM(s) mark active gene body?

Answer 13

H3K36me3

Question 14

H3K27ac vs H3K27me3

Answer 14

enhancer vs repressed promotor

Question 15

What is ChipSeq ?

Answer 15

Chromatin Immuno Precipitation Sequencing
https://www.youtube.com/watch?v=nkWGmaYRues

Question 16

What does it mean if ChipSeq shows multiple different PTMs at the same site?

Answer 16

1. Population has different PTMs
2. Two repeating histone types in a nucleosome have different PTMs

Question 17

Bivalent genes?

Answer 17

Genes with PTM markers for both activation and repression (poised/undecisive) => they can further differentiate in either when one PTM is removed. Bivalent genes are lineage specific/developmental genes regulative

Question 18

Histone modifying enzymes?

Answer 18

Writers, readers, erasers

Question 19

writer examples?

Answer 19

HAT: acetylate Lys (Histone AcetylTransferase
KInases: phosphorylate Ser/Thr
PRMT: methylate Arg (Protein aRginine MethylTransferases)
KMT: methylates Lys

Question 20

reader domain examples?

Answer 20

Bromo: Ac
SANT: P
Tudor: Me
Chromo: Me

Question 21

eraser examples?

Answer 21

HDAC: remove Ac Lys(Histone DeAcetylases)
PPTase: dephosphorylates
PAD: PeptidylArginine deiminases (Introduce Citruline???)
KDM: removes Me (Lysine DeMethylase)

Question 22

Examples of chromodomains?

Answer 22

CHD-1 (H3K4me): ATP-dependent chromatin remodeler
HP1 (H3K9me): essential heterochromatin protein, recruits DNMT1 (DNA methylation)
CBX2 (H3K27me): subunit of PRC1 that reads H3K27me3, while another subunit establishes
H2AK119ub1 (another PTM)

Question 23

Set1 activation pathway?

Answer 23

Cfp1(CXXC motif) binds to un-methylated DNA
Cfp1 recruits Set1
Set1 methylates H3K4
H3K4me3 inhibits DNMT3A/L binding
preventing DNA methylation: region
remains ACTIVE.

Question 24

HP1 DNA inactivation pathway?

Answer 24

Suv39 methylates H3K9
H3K9me3 is bound by HP1
HP1 recruits DNMT1
DNMT1 lays down DNA methyl groups
DNMT1 also recruits HDACs
HDACS remove active histone H4K16ac
Result: chromatin compaction and
region is INACTIVE.

Question 25

PRC1 inactivation pathway?

Answer 25

PRC2 establishes H3K27me3, which is then read by PRC1 which
establishes H2AK119ub1

Question 26

the most crucial effects of chromatin template transitions

Answer 26

cis effects: brought about by changes in the physical properties of modified histone tails, such as a modulation in the electrostatic charge or tail structure that, in turn, alters internucleosomal contacts.

trans effects: the recruitment of modification-binding partners to the chromatin.

histone variant exchanges: signaling the replacement of a core histone with a histone variant

Question 27

when are histones added to DNA?

Answer 27

S phase. DNA daughter strands are
generated and histones are recruited to them to form new nucleosomes.