Histone modifications and where to find them

A cheat sheet for which histone modification marks which genomic element.

Do you ever wonder, ”Where was that histone modification found again? Was it an active promoter or enhancer?” If so, we’ve put together this guide for you so that you never have to go back to the literature to find out!

We’ve listed the most common histone modifications and which genomic regions they mark, ie where you can expect to find them in your ChIP/ChIPseq experiments. To give that little bit extra, we’ve also listed for you the most specific antibodies that recognize those histone modifications.

Histone markWhere to find itAntibody
H3K4me1Active enhancersab176877
H3K4me3Promoters of active genes, bivalent domainsab213224
H3K9acActive enhancers and promotersab177177
H3K27acActive enhancers and promotersab177178
H3K36me3Transcribed regionsab9050
H3K79me2Transcribed regionsab177184
H3K9me3Heterochromatin, satellite repeats, gene-poor regionsab176916
H3K27me3Repressed promoters in gene-rich regions, developmental regulators, bivalent domainsab192985
Gamma H2A.XDNA double-strand breaksab81299
H3S10PWhole chromosomes in mitosisab177218
H4K16acReduced in cancer at repetitive sequences, active genes and enhancers in ESCs. Inhibits formation of high order chromatin structure.ab109463

Green = generally associated with transcriptionally active regions; red = generally associated with transcriptionally repressed regions; grey = other functions.


  • 1. Greer, E. L. & Shi, Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat. Rev. Genet. 13, 343–57 (2012).
  • 2. Voigt, P., Tee, W.W., and Reinberg, D. A double take on bivalent promoters. Genes Dev. 27, 1318-1338 (2013).
  • 3. Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I., and Zhao, K. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837 (2007).
  • 4. Kim, J. & Kim, H. Recruitment and biological consequences of histone modification of H3K27me3 and H3K9me3. ILAR J. 53(3-4):232-9 (2012).
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