H3K9ac
H3K9ac is an
The H3K9 histone has two jobs. Genes get turned on if this mark is acetylated and silences them if methylated. H3K9ac is an important acetylation and connected with active promoters. H3K9ac and H3K14ac have been shown to be part of the active promoter state. They are also present over bivalent promoters and active enhancers.
This is also a mark for liver cancer through a defect in the H3K9ac/H3K9me3 transition.
Lysine acetylation and deacetylation
Proteins are typically acetylated on lysine residues and this reaction relies on acetyl-coenzyme A as the acetyl group donor. In
The regulation of transcription factors, effector proteins,
In the field of
Nomenclature
H3K9ac indicates acetylation of lysine 9 on histone H3 protein subunit: [6]
Abbr. | Meaning |
H3 | H3 family of histones |
K | standard abbreviation for lysine |
9 | position of amino acid residue (counting from N-terminus) |
ac | acetyl group |
Histone modifications
The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as
Epigenetic implications
The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a Histone code dictates the expression of genes by a complex interaction between the histones in a particular region.[9] The current understanding and interpretation of histones comes from two large scale projects: ENCODE and the Epigenomic roadmap.[10] The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together. Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of
The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This additional level of annotation allows for a deeper understanding of cell specific gene regulation.[14]
H3K9ac
H3K9ac and H3K14ac have been shown to be part of the active promoter state. They are also present over bivalent promoters and active enhancers.[15]
The H3K9 histone has two jobs. Genes get turned on if this mark is acetylated and silences them if methylated. H3K9ac is an important acetylation and connected with active promoters.[16]
This is also a mark for liver cancer through a defect in the H3K9ac/H3K9me3 transition.[17] Also, lower acetylation at this mark shows a poor prognosis in oral cancer.[18]
Methods
The histone mark acetylation can be detected in a variety of ways:
1. Chromatin Immunoprecipitation Sequencing (
2. Micrococcal Nuclease sequencing (MNase-seq) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences.[20]
3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive
See also
- Histone acetylation
- Post-translational_modification#Addiction
References
- PMID 17681659.
- PMID 16289629.
- PMID 18722172.
- PMID 2736326.
- PMID 3733880.
- ISBN 9780127999586.
- PMID 18037899.
- PMID 17320507.
- S2CID 1883924.
- PMID 17571346.
- PMID 20888037.
- PMID 21177974.
- PMID 21179089.
- PMID 25693563.
- PMID 22920947.
- ^ "Histone H3K9 Review". Epigenie. Retrieved 16 December 2019.
- PMID 31097476.
- S2CID 205171548.
- ^ "Whole-Genome Chromatin IP Sequencing (ChIP-Seq)" (PDF). Illumina. Retrieved 23 October 2019.
- ^ "MAINE-Seq/Mnase-Seq". illumina. Retrieved 23 October 2019.
- PMID 25559105.
- PMID 26314830.
- PMID 20150147.