H3K4me3

H3K4me3 denotes a specific chemical modification of proteins used to package DNA in eukaryotic cells (including human cells). The proteins, known as histones, are major components of chromosomes. This modification is commonly associated with active transcription of nearby genes.^[1]

Nomenclature

H3K4me3 means trimethylation of lysine 4 on histone H3 protein subunit:

Abbr.	Meaning
H3	H3 family of histones
K	standard abbreviation for lysine
4	position of amino acid residue (counting from N-terminus)
me	methyl group
3	number of methyl groups added

Epigenetic marker

A lysine specific histone methyltransferases (HMT) transfers three methyl groups to histone H3. H3K4me3 is used as a histone code or histone mark in epigenetic studies (e.g., chromatin immunoprecipitation ChIP-seq) to identify active gene promoters. H3K4me3 histone modification is found in high abundance in the cells. H3K4me3 is highly enriched at active promoters near transcription start sites (TSS).^[2]

Lysine methylation

The following diagram shows 3 methyl groups (—CH₃) added to lysine, replacing hydrogen atoms:

• 

  Unmethylated lysine

• 

  (6-N,6-N,6-N)trimethyllysine

Incremental methylation of lysine residue (dashed line denotes peptide backbone):

H3K4me3 modification corresponds to the rightmost diagram, above trimethyllysine label.

See also

• Histone methylation
• Histone methyltransferase
  • SET domain-containing lysine-specific
• Methyllysine
• JARID1B, an enzyme which can reverse the methylation
• PHD finger, a protein domain reported to interact with H3K4me3
• Bivalent chromatin, where this activating modification is often used together with repressor H3K27me3

References

1. Guenther, Matthew G.; Levine, Stuart S.; Boyer, Laurie A.; Jaenisch, Rudolf; Young, Richard A. (2007-07-13). "A chromatin landmark and transcription initiation at most promoters in human cells". Cell. 130 (1): 77–88. doi:10.1016/j.cell.2007.05.042. ISSN 0092-8674. PMC 3200295. PMID 17632057.
2. Liang, G (2004). "Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome.". Natl Acad. Sci. USA. 101: 7357–7362.