Lecture 23 DNA methylation and Chromatin remodeling

Bacterial DNA methylation

N6-methylation

Bacterial DNA methylation function

DNA replication defense

Eukaryotic DNA methylation

5-Methylcytosine

Eukaryotic DNA methylation function

gene silencing

In mammals, where does methylation most commonly occur?

At C in CG dinucleotides

Where does methylation most commonly occur in plants?

at C in CNG trinucleotide

what enzymes perform methylation?

DNA methyltransferases (DNMTs)

DNMT1

maintenance DNMT

the frequency of CpG dinucleotide occurence in the human genome is ___ than expected; why?

lower due to deamination

deamination involves the conversion of cytosine to…

thymine or uracil

CpG island

region of genome where Cpg content is at or above expected levels

Are CpG islands easily mutated?

no; they are functionally important sequences so mutation is not tolerated

Where are CGI (CpG islands) found?

at 70% of promoters

What happens when CpG is methylated?

gene silencing/heterochromatin

How does CpG methylation cause silencing?

by blocking DNA binding or via Methyl-CpG binding proteins

Where do many transcription factors contain CpG dinucleotides?

in their DNA binding motif

MeCP2

Methyl CpG binding proteins

MBD

methyl DNA binding domain

TRD

transcription repression domain

Which two enzymes contribute to the repression of transcription?

DNMTs and HMTs

HMTs

enzymes that carry out histone methylation (histone methyl transferases)

Where are DNMTs recruited in heterochromatin and what do they do?

recruited to the promoter, methylate CpG

once CpG is methylated, what binds DNA? what does this recruit?

MBD protein binds and HDAC corepressor is recruited

Name four diseases caused by DNA methylation

1. Rett syndrome

2. ICF syndrome

3. imprinting disorders

4. cancer

What methyl Cpg binding protein is involved in Rett syndrome?

MECP2

What methyl Cpg binding protein is involved in ICF syndrome?

CNMT3b

euchromatin contains genes that are ___

active

heterochromatin contains genes that are ____

silent

Chromatin remodeling subfamilies are organized based on…

ATPase subunit

SWI/SNF chromatin remodeling subfamily

most activators

ISWI and CHD chromatin remodeling subfamily

most repressors

INO80 chromatin remodeling subfamily

histone exchange

SWI yeast mutant

mutants that cannot switch mating type

snf yeast mutant

mutants that cannot ferment sucrose (sugar no fermentation)

what do swi and snf mutants tell you about their chromatin remodeling complexes?

genes required for mating type switch and sucrose fermentation required remodeling at their promoters

How are targeting remodeling complexes recruited to target sites?

by sequence specific factors; cannot recognize target sites themselves

How are nucleosomes adjusted to allow access to the DNA that they contain?

energy dependent chromatin remodeling

four types of chromatin remodeling

1. nucleosome sliding

2. histone exchange

3. nucleosome eviction

4. altered structure

Pho system

Under phosphate starved conditions, bHLH binds UASp1, which then recruits a nucleosome evicting chromatin remodeling complex, exposing UASp2

are histone modifications permanent?

no; they are reversible

At which point during the cell cycle are kinases activated?

in G2

At which point in the cell cycle do phosphatases act?

early in G1

HAT

histone acetyl transferase

HDAC

histone deacetylase

name three different targets of histone modifying enzymes

1. histones directly

2. transcription activators

3. histone remodeling complexes

What recruits Histone acetyl transferases during histone acetylation?

activator

result of histone acetylation

chromatin opens and becomes euchromatin

What recruits Histone Deacetlyase to chromatin?

repressor

CBP is what kind of enzyme?

a histone acetlyase

histone modification enzymes are a part of ____ machinery

transcription