BIMM 112 - Chromatin Vocab, Histone Modifications, and Important Assays

Acetylation of Histone Lysine Residues

Lysine rich tail binds tightly to DNA, blocks DNA access for transcription. Acetylation of these lysines unblocks the DNA.

Acetylation as a Transducing Signal

Acetylation of a histone at a location on a protein or other molecule may eliminate/create recognition sites

Acetylation effects on a Nonhistone protein

Affects overall activity of protein broadly

Writers

Enzymes that add modifications to proteins

Erasers

enzymes which remove the modification

Readers

proteins that recognize and bind to the modification

Histone acetylation correlates to..

gene activation

Trimethylation of H3K4 (H3K4me3 in promoter regions) and H3K36 (H3K36me3 in transcribed regions/gene bodies) correlates to…

gene activation

Trimethylation of H3K9(me3) correlates to…

heterochromatin (transcriptional) gene repression

Trimethylation of H3K27(me3) correlates to…

polycomb-mediated gene repression (Polycomb Repressive Complexes 1 (reader), 2(reader and writer of me3) [PRC 1,2])

H3K4me1 and H3K27ac are seen at..

active transcriptional enhancers

ChIP-seq

Chromatin-immunoprecipitation sequencing. Identifies protein binding sites and enable analysis of transcription factors, histone modifications, and chromatin states

SAM

S-Adenosyl Methionine, Histone methylase cofactor

Acetyl-CoA

Acetyl Coenzyme A. Histone acetylase cofactor

Rpd3

Histone-deacetylase. No cofactor needed

LSD-1

Demethylase that uses FAD as a cofactor

JHDM

Demethylase that uses Fe(II) as a cofactor