Lecture 9: Histone Code Chromatin and Modification

Histone methylation can be part of what?

both heterochromatin and euchromatin

True or False: Acetylation is always associated with active chromatin, and deacetylation is associated with inactive chromatin.

true

What does H3K9ac do?

makes the chromatin more open

Can acetylation and methylation occur at the same time?

no, it cannot

True or False: Phosphorylation is associated with both euchromatin and heterochromatin.

true

What does HP1 read?

H3K4me3

What do chromodomains do?

recognize and bind to methylated lysine sites on chromatin

What do chromodomains associate with?

silent chromatin

What kind of site do chromodomains contain?

a H3K9me site

Where do bromodomains bind and recognize?

acetylated lysines

What are acetylated lysines associated with?

active chromatin

Evidence for how nucleosomes and transcriptional activators occur was derived from what?

mutations of a gene called SWI2 and SNF2

What did a mutation in Swi2/Snf2r result in?

reduced transcription of the HO and SUC2 gene

What does the HO gene code for?

a DNA endonuclease that is required for mating type switching

What does the SUC2 gene code for?

invertase that uses sucrose as a source of carbohydrates

What could the mutations in Swi2/Snf2 be suppressed by?

mutations in histone H4, but mutations in any core histone would have the same effect

What was the hypothesis of the Swi2/Snf2 study?

SWI2/SNF2 played a role in gene expression by modulating chromatin structure

Swi2/Snf2 acts as a what on the core histone proteins?

an inhibitor

True or False: It was later found that the SWI2/SNF2 protein is a component of a large multi-protein complex that could disrupt or reconfigure nucleosomes and stabilize the binding of TFs to nucleosomal DNA; this complex was named the SWI/SNF complex.

true

What does the SWI/SNF complex act as?

as an ATP-dependent chromatin remodeling factor complex

What does the SWI/SNF complex bind?

binds both DNA and nucleosomes in the nm range with high affinity

What does the SWI/SNF complex generate?

nucleosome-free regions by promoting unwinding of the DNA around the nucleosome and by sliding nucleosomes along DNA with ATP hydrolysis to promote transcription

The SWI/SNF complex is what?

a conserved complex

What does experimental evidence suggest about activaors?

• An activator must find access to its binding site on chromatin

  • Transcription factor must be activated and is the one that facilitates the recruitment of the remodeling complexes to the chromatin

• This activator recruits remodeling complexes (and other factors)

  • SWI/SNF complex

• The holoenzyme is then recruited to form the pre-initiation complex

What are the two types of transcription factors?

pioneer and general TFs

What is important to know about pioneer TFs?

• Essential for most cellular function

• Has the ability to bind to the DNA even when DNA is bound to nucleosomes

• Initiates of lot of signal transduction, development, etc

What is Swi5?

the pioneer TF that recognizes enhancer sequences embedded in the chromatin

What does Swi5 act as?

a dimer

What is the Swi5 process?

1. Swi5 finds access to its binding sites

2. Swi5 recruits the Swi/Snf complex

3. Chromatin remodeling by Swi/Snf leads to the recruitment of the SAGA complex

4. SAGA facilitates HATs to open up the chromatin

5. Remodeling by Swi/Snf and hyper-acetylation of histone tails by SAGA results in the opening of chromatin and the recruitment of the TF SBF

6. SBF is implicated in the recruitment of GTFs

True or False: Sometimes the pushing and pulling of nucleosomes can actually result in transcription silencing; the amount of nucleosomes can be pushed towards an enhancer sequence —> evidence for this restricting transcription.

true

What are the three types of co-activators?

• chromatin remodeling complexes

• histone acetyl transferases (HATs)

• mediator

How are histone acetyl transferases similar to chromatin remodeling complexes?

• conserved from yeast to human

• neither binds DNA directly

• can bind modified histones

What two major HDAC complexes do yeast have?

HDA and HDB

What is the catalytic subunit of HDA?

HDA1

What is the catalytic subunit of HDB?

RPD3

What type of modification is important in cancer?

deacetylation—removing deacetylation activity can control tumor suppressor activity

How many different families of yeast HDACs are there?

5 different classes

What is included in class 1?

HDACs 1, 2, 3, and 8

What type of enzymes make up class 1?

RPD3-like enzymes

What is included in class 2a?

HDACs 4, 7, and 9

What type of enzymes make up class 2a?

HDA1-like enzymes

What is included in class 2b?

HDAC 6 and 10

What type of enzymes make up class 2b?

HDA1-like enzymes

What is included in class 3?

sirtuins 1-7

What type of enzymes make up class 3?

sir2-like enzymes

What is included in class 4?

HDAC II

What is important to know about CpG islands?

• cytosines are methylated

• CpG islands are core promoters

What does methylation of cytosine residues impact?

transcriptional activity

What are methylated cytosines recognized by?

the protein MeCP2

What does MeCP2 do?

recruits HDACs by interacting with the Sin3A subunit of the complex

True or False: In general, CpG islands have a repressive transcription action.

true