Epigenetics:Histone Modification I

Nucleosome

• A packaging unit for DNA (=H3/H4 tetramer + two sets of H2A/H2B dimer)

• DNA (- charge) and histones (+ charge)

• histones = tails and globular domains

Higher-Order Packaging of Chromatins

• An efficient packaging strategy (10,000-fold compaction)

• A barrier for gene transcription

Three strategies to change nucleosome arrangement

• used for regulating gene transcription

• cis-effects: acetylation-driven activation

• trans-effects: reader-driven transcriptional control

• Nucleosome repositioning and displacement – ATP-driven reaction

Various histone modifications

• H3 and H4 are most modified

• Lys and Arg are most frequent targets

• Acetylation on Lys: activation

• Methylation on Lys: activation or repression

• Methylation on Arg: repression

• Ubiquitylation: repression

• Phosphorylation on Ser Thr: cell cycle signal

Major enzymes for histone modifications

- Modifications are reversible(HAT vs HDAC, Kinase vs PPase)

- Methylation on Lys has different states (mono, di, tri)

- Methylations are very stable

Consequences of histone modifications

- Modification on each amino acid hasa different meaning

- Two different modifications on one amino acid are exclusive and have opposite signals (K27me3 vs K27ace)

- Readers (Acetylation- Bromo proteins,Methylation- Chromo proteins)

- Main epigenetic regulators Polycomb (repression memory) H3K27me and H2AK119ub Trithorax (activation memory)H3K4mePosition Effect Variegation(repression) H3K9me

Polycomb mutant

Sex com in the front legs of male flies

Pc mutants have sex comb in other legs-> homeotic transformation mis-expression of Hox genes

Polycomb-Group (PcG) genes control Hox genes and other developmental genes

Main repression mechanism -> provides“cellular memory or transcriptional memory”

Cellular memory

- Mammals 200 cell types vs plants 30 cell type

- Different cell types have their own identity in terms of transcriptional programs

- Epigenetic modifications serve as amolecular basis for cellular memory

Cellular memory

- Early genetic studies identified two types of fly mutants

- Polycomb mutants – defects with repression memory (H3K27me3 and H2AK119ub)

- Trithorax mutants – defects with activation memory (H3K4me3)

PcG mutants- a & b – imaginal disc

- c & d – suz12 mutant

- e & f – Ring1A mutant

Core PcG genes

PRC2 well conserved

PRC1 only in metazoans

Many duplications of PRC2members in plants

Core PcG genes of PRC2- three main components Ezh1/2, Suz12, Eed

Ezh1/2- HMT enzyme Eed – glue protein Suz12 – no function yet

- several other proteins RbAp48/49, Jarid2, Aebp2

RbAp48/49 – histone binding Jarid2 – DNA binding Aebp2 – DNA binding

PcG-dependent repressionPRC2 -> H3K27

H3K27 -> PRC1

PRC1 -> H2AK119ub

Targeting of PRC2 & PRC1 ismediated either by ncRNA orDNA-bindig protein

Maintenance of H3K27me3 during DNA replication is mediatedthrough Eed

Genome-wide PRE sites

- more than Hox cluster

- many genes with tissue-specificgenes are controlled throughPRC-mediated mechanisms

- PRC2 serves as temporaryrepression mechanism (poised state) in early stage embryo

- modify CpG islands