L9_Histone Modifications: Histone Methylation

Histone methylation refers to methylation of:

-lysine residue

-arginine residues

-histidine residues

Both lysine and arginine have methylation roles in___________regulation.

epigenetic gene

Lysine can be________________________methylated at the ε-amino group

mono, di, tri

(same position that gets acetylated at the ε-amino groups)

Histone methylation is carried out by ________________.

histone methyltransferases (HMTs)

1. HKMT

2. PRMT

HKMT

Histone Lysine Methyltransferase

PRMT

Protein Arginine Methyltransferases

_____________ is the donor of methyl groups in histone methylation.

S-adenosylmethionine (AdoMet)

same donor used in DNA methylation

Arginine can be_______________ methylated.

1. mono

2. symmetrically di

3. asymmetrically di

Major Lysine Methylation Marks on the amino-termini of histone________ and _______.

H3 and H4

Di and tri methylation function marker in Lysine methylation marks

promoter or activation

Mono methylation function marker in Lysine methylation marks

enhancer

__________ and _________ appears to play an important roles in marking promoters and gene bodies during active transcription during lysine methylation

H3K4 and H3K36

Histone Lysine Methyltransferases (HKMT’s) two broadly families

1. SET domain carrying HKMT

2. Dot1-like HKMTs-do not contain SET domain

_____________was identified as shared sequence motif in 3 drosophila genes. 

SET domain 

SET domains found in which 3 drosophila genes?

1. suppressor of variegation (Su(var)3-9)

2. enhancer of zeste (E(z))

3. homeobox gene regulator thrithorax (Trx)

Over___genes carry set domain

50

Dot1-Non SET domain HKMT methylates ________.

H3K79

usually found in yeast, but has also been found in humans. 

_________mono-methylate H3K4 but can add additional methyl groups 

SET 7/9

Polycomb Repressor Complex 2  PRC2 is also known as__________? 

Polycomb group of PcG

PRC2 (Polycomb Repressor Complex 2) function:

• confers H3K27 di and trimethylation

• initially identified in drosophila

• methylation is maintained by PRC1

Drosophila PRC2 has conserve core of which four proteins?

1. E(Z)=enhancer of zeste

2. ESC=extra sex comb

3. SU(Z)12=suppressor of zeste

4. NURF55

__________

1. First HMT identified in humans-ortholog of Su(var)3-9

2. causes H3K9 trimethylation

3. identified drosophila due to suppression of position effect variegation 

SUV39H1

_____________________

1. main effector of H3K4 trimethylation

2. ortholog of drosophila trithorax 

Mixed Lineage Leukemia (MLL) 

Proteins of _________binding domains recognize histone methylation

methyl

Readers of Lysine Methylation

1. plant homeodomain (PHD) fingers

2. bromo-adjacent homology (BAH) domain

3. royal superfamily proteins

What are the royal superfamily proteins?

• chromodomains

• tudor

• double tudor

• PWWP domain

PHD finger reads________

H3K4me3

• part of NURF (nucleosome remodeling factor) complex

• involved in chromatin remodeling

_________ is an example of DNA and histone working together. It is a DNA Methyltransferase that causes CHG methylation specific to plants only.

CMT3

______Domain is found in MTA1 (member of the NURD complex), and in plant chromomethylase CMT3.

BAH

Royal Superfamily of lysine methylation readers chromodomain functions: 

• ex: histone protein1 (HP1)

• HP1 and H3K9 were found to colocalize on heterochromatin

• in plants HP1 ortholog LHP1 is found to coexist with H3K27me3

Functional Outcomes of Reading Histone Marks

1. architectural proteins

   1. Sir2

   2. HP1

   3. PRC1

2. chromatin remodelers

   1. NURF (PHD)

   2. SWI/SWF

3. chromatin modifiers

   1. K20me1-read by PWWP domain of PDp1-recruits

   2. Set9 (KMT)-convert K20me1—> K20me3

   3. Dnmt3 has PWWP domain-binds to K36me3

4. adaptors

   1. transcription

   2. repairs

   3. recombination

   4. replication

   5. RNA processing

How do erasers in lysine methylation work?

1. Oxidation

2. Hydroxylation

Oxidation Eraser in Lysine Methylation

_______________demethylates lysine using FAD (flavin adenine dinucleotide) as a cofactor

amine oxidation

Oxidation Eraser in Lysine Methylation

______________

demethylates H3K4me2/me1 and H3K9me2/me1

lysine specific demethylation (LSD1)

Oxidation Eraser in Lysine Methylation

__________demethylates H3K4me2/me1

LSD2

Hydroxylation Eraser in Lysine Methylation:

____________

domain containing iron dependent dioxygenases

Jumonji C (jmjC)

Jumonji domain demethylates ________, __________, ___________.

H3K9me2, H3K27me, and H4K20me1

Specific DNA sequence elements have been identified for some of the proteins, these include:

1. Trithorax group response elements (TRE)

2. Polycomb group PcG

Trithorax group response elements recruit ____.

TRX

an H3K4 methyltransferase

Polycomb group (PcG) response elements (PREs) and PcG proteins (e.g) PRC2 catalyze__________.

H3K27me2/3

Long non coding RNAs (IncRNAs) have also been shown to bind to certain _______ and _________ methyltransferases.

H3K4 and H3K9

• ex. human incRNA HOTAIR binds to PRC2 (H3K27me2/3)

• H3K4 methyltransferase to repress target genes

In certain organisms like fission yeast___________ is required for maintaining centromere heterochromatin.

RNA interference (RNAi)

Fission yeast does not have DNA methylation thought.

______ is a chromodomain protein required for silencing heterochromatic regions targeted by RNAi (linking RNA 2kb).

it was also found to be a component of RNA induced transcriptional silencing (RITS)

Chp1

DNA methylation: certain methyltransferases (H3K9 methyltransferase) bind to methylated________- via methyl binding domain. 

cytosine

Loss of MBD leads to loss of _________methylation.

H3K9

Histones on newly synthesized DNA can be immediately modified.

Some of the _______ remain associated with DNA during replication

HKMTs (eg. MLL, PcG)

_____________ is when each daughter chromosome inherits half of the nucleosome and guide methylation of newly synthesized histones

semi-conservative manner (a)

_____________nucleosomes segregate to both strands, where methylation marks are copied using neighboring marked histones

intact

__________guides histone methylation

DNA methylation

Histones are _____________ before assembly into nucleosome

pre-marked

Meiotic Inheritance is also known as ___________________

trans-generational

___________has been shown to help inherit methyl marks in C. elegans.

RNAi

In limited cases, histone methylation marks themselves can pass through meiosis.

High levels of expression of certain genes pass from mother to daughter in amoebas.

Knocking down__________ methyltransferase knocked out such behavior

H3K4

Knocking out _____________________ in C elegans lead to progressive increase H3K4me2 levels

SPR-5

each generation of mutant worms are normal but become progressively sterile over many generations 

_________ and __________ coexist

DNA methylation and H3K9

DNA methylation requires loss of _________

H3K9 methylation

H3K4me2/me1 demethylase LSD1 is required for _______DNA methylation

global

LSD2, another H3K4me2/me1 demethylase is required for _______________mediated by DNA methylation.

genomic imprinting

___________connects to DNA methylation to non methylated H3K9. 

Dnmt3L

Dnmt3L recruits __________ to that stretch of DNA and methylates cytosine

Dnmt3a

MLL1 links H3K4 methylation to_________

non methylated CpGs

What is MLL1 and it’s function in DNA methylation and histone modification?

Set domain containing protein that causes H3K4me3

• loss of MLL causes loss of H3K4 methylation and de novo DNA methylation in mice

• contains domain that bonds specifically to non methylated CpG

____________jumonji domain protein-links non-methylation of DNA and H3K36.

JHDM1

Function of JHDM1

binds to non-methylated CpG and demethylates H3K36me2

DNA methylation depends on H3K9 methylation in ______ and __________.

fungi and arabidopsis

________________ a H3K9 methyltransferase binds to directly methylated CHG residues

KRYPTONITE (KYP)

KYP is a SU (var)3-9 homolog containing ____________

SET domain

______________is responsible for CHG methylation, binds H3K9me2-containing nucleosomes. This is associated with BAH and chromodomains within the same polypeptide.

CHROMOMETHYLASE3 (CMT3)

H3K9 methyltransferases _______ and ______ are involved in DNA methylation in mammals.

G9a and GLP

________ and _____ methylation and ______ are interdependent and bidirectional in plants.

CHG and CHH; H3K9me2

CMT3 maintains ___ methylation

CHG

CMT2 maintains____ and ______ methylation

CHG and CHH

prefers unmethylated DNA as substrate

CMT2- and CMT3- mediated maintenance of DNA methylation is dependent on ________

H3K9me2

both _____ and _______ domains carry binding sites for H3K9me2

BAH and chromo

H3K9me2 through KTP depends on ______

CMT3

• loss of CMT3—> leads to loss of H3K9me2

KYP binds to methylated cytosine via cytosine via _________domain.

SRA

H3K9me3 methylation unidirectionally control DNA methylation in Nuerospora.

_________encodes a H3K9 methyltransferase. It is apart of the DCDC complex that causes H3K9me3.

DIM-5

H3K9me3 attracts______. Which then recruits DIM-2 for a unidirectional interaction.

HP1

H3K4 and H3K9 methylation are _______.

Antagonistic (inverse correlation)

in H3K9 Methylation

_______has 2 domains, PHD domains bind to H3K4Me3, and the jumonji domain demethylates H3K9me2.

PHF8