Epigenetics_10.20

• Swi/snf (switch/sniff)
• named after the swi mutants in yeast that are unable to switch mating type, and snf mutants that are sucrose non-fermenting

SWI/SNF

ISWI

INO80/SWR1

• clearing the promoter from histones
• 

• sliding nucleosomes onto the promoter region
• 

Sliding: CRC exerts force on the DNA making the DNA slide along the histone core

Conformational change: CRC alters the conformation of the histone octamer and its association with DNA

Nucleosomes are not static: their dynamic nature allows nucleosomal DNA to transiently unwrap and rebind the histone octamer and thus gives TFs transient access to DNA

Furthermore, some smaller TFs can bind to DNA while it is still wrapped around histones!

TFs then recruit chromatin remodeling complexes to shift nucleosomes and free up space for the more bulky factors to bind

Transcription activation often involves nucleosome displacement at the promoter

Under low phosphate conditions, a bHLH TF Pho4 induces displacement of four nucleosomes in the promoter of PHO5 in a SWI/SNF and INO80-dependent manner

This displacement frees up the TATA box and enables transcriptional activation of the PHO5 gene by Pho2 and Pho4 transcriptional activators

regions of the genome that bind TFs

• acetylated
• methylated
• phosphorylated
• ubiquiniated

Methylation does not erase the positive charge of these amino acids

Phosphorylation adds negative charge to the amino acids

The histone code describes the combinatorial modification status of a one or more nucleosomes in the chromatin

Combinations of histone marks have a cumulative or collective impact on chromatin structure and function and are referred to as the histone code

• chromodomain proteins
• bromodomain proteins

Modification of specific histones at specific positions define different structural states of chromatin

• acetylation
• The acetyl group is removed when they become nucleosomes

Acetylation neutralizes the positive charge of NH3 and thus disrupts the interaction between histone tails and negatively charged DNA

• If the H3 histone is methylated at site K-4, its indication is transcription activation
• Modifying the H3 histone:
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combinations of histone marks can have a cumulative or collective impact on chromatin structure and function

• Histone tail interactors
• recognized methylated lysines

• CHDs (chromodomain)
• PHD (plant homeodomain)
• Tudor domain

• readers
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• writers
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• erasers
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Lysine acetylation

• histone acetyltranferases (HATs)
• correlated with transcriptional activity

• histone deacetylases (HDACs)
• correlated with transcriptional repression

• lysine and arginine residues
• associated with transcriptionally active chromatin

Bromodomain proteins

Is associated with transcriptionally silent chromatin

Requires prior deacetylation by HDAC

Leads to changes in charge

Linked to condensed chromatin in mitosis but to activation of some genes in interphase!

Found in all eukaryotes

For example, the canonical H2A histone is replaced by the H2AX variant in sites of DNA damage and is thought to facilitate DNA repair: its phosphorylated form g-H2AX stabilizes binding of repair factors at DNA breaks and maintains checkpoint arrest

C5 position of cytosine

CG suppression (i.e., elimination of CpG dinuclotides from the genome in evolution) is a consequence of spontaneous oxidative deamination of methylated cytosines to thymines over time

In genes that are expressed CpG islands are usually unmethylated, but methylation can silence gene expression

condensed chromatin

bisulfite mutagenesis and sequencing