Histone modifications: a guide

Histone modifications are post-translational modifications that regulate gene expression, with histone H3 being the most modified histone.​​

Post-translational modifications to histones – referred to as marks – regulate gene expression by organizing the genome into active regions of euchromatin, where DNA is accessible for transcription, or inactive heterochromatin regions, where DNA is more compact and less accessible for transcription. 

Histones pack and order DNA into structures known as nucleosomes so that it fits within a cell’s nucleus. Each nucleosome contains two subunits, both made of histones H2A, H2B, H3 and H4 – known as core histones – with the linker histone H1 acting as a stabilizer.

Histone H3 is the most modified histone. Modifications to histone H3 can predict the type of chromatin (heterochromatin vs euchromatin), distinguish between functional elements of the genome (promoters, enhancers, gene bodies), and determine whether these elements are in an active or repressed state.

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Figure 1. The most common histone modifications. See our histone modifications poster for more.

When investigating histone H3 modifications the most useful control to look at, is the total histone H3. 

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Histone methylation​​

Lysine methylation of H3 and H4 is implicated in both transcriptional activation and repression depending on the methylation site, while arginine methylation promotes transcriptional activation1.

Lysines can be either mono-, di-, or tri-methylated, providing functional diversity to each site of methylation. For example, both mono- or tri-methylation of K4 (H3K4me1 or H3K4me3) are active marks, but H3K4me1 is found at transcriptional enhancers, while H3K4me3 is found at gene promoters. Tri-methylation of K36 (H3K36me3) is associated with transcribed regions in gene bodies.

Tri-methylation of K9 and K27 on histone H3 (H3K27me3 and H3K9me3) are both repressive signals, however, H3K27me3 is a temporary signal that controls development regulators. Conversely, H3K9me3 is a permanent signal for heterochromatin formation of chromosomal regions with tandem repeat structures.

H3K27me3 is found primarily at promoters in gene-rich regions, and is closely associated with developmental regulators in embryonic stem cells, including Hox and Sox genes. H3K9me3 is generally found in gene poor regions such as satellite repeats, telomeres and pericentromeres. It also marks retrotransposons and specific families of zinc finger genes (KRAB-ZFPs).

Both marks are found on the inactive chromosome X, with H3K27me3 at intergenic and silenced coding regions and H3K9me3 predominantly in coding regions of active genes. 

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Histone acetylation

Histone acetylation is often associated with an open chromatin structure. This makes chromatin accessible to transcription factors and can significantly increase gene expression2.

Histone acetylation is largely targeted to promoter regions. For example, acetylation of K9 and K27 on histone H3 (H3K9ac and H3K27ac) is normally associated with enhancers and promoters of active genes. Low levels of acetylation are also found throughout transcribed genes, although the function of this is still unclear.

Histone acetyltransferases (HAT) and deacetylases (HDACs) are the enzymes responsible for writing and erasing the acetylation of histone tails. Lysine residues within histone H3 and H4 are preferential targets for HAT complexes. 

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Histone phosphorylation

Phosphorylation of core histones is a critical intermediate step in chromosome condensation during cell division, transcriptional regulation, and DNA damage repair3–6. Unlike acetylation and methylation, histone phosphorylation seems to function by establishing interactions between other histone modifications and serving as a platform for effector proteins. This leads to a downstream cascade of events.

Phosphorylation of histone H3 at S10 (H3phosphoS10) and histone H2A on T120 are mitotic markers: these modifications are involved in chromatin compaction and the regulation of chromatin structure and function during mitosis. Phosphorylation of H2AX at S139 (resulting in γH2AX) has been identified as one of the earliest events occurring after DNA double-strand breaks and serves as a recruiting point for DNA damage repair proteins7,8.

Histone phosphorylation also has a broader role to play: H2B phosphorylation, for example, facilitates apoptosis-related chromatin condensation, DNA fragmentation, and cell death9.

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Histone ubiquitylation

Histone H2A and H2B are two of the most highly ubiquitylated proteins found in the nucleus10. The most abundant forms are monoubiquitylated H2A on K119 and monoubiquitylated H2B on K123 (yeast)/K120 (vertebrates). However, polyubiquitylated histones have also been described, such as K63-linked polyubiquitylation of H2A and H2AX.

Monoubiquitylation of H2A is catalyzed by polycomb group proteins, and it is mostly associated with gene silencing. The main enzyme responsible for monoubiquitylated H2B is Bre1 in yeast and its homologs RNF20/RNF40 in mammals. Unlike H2A, monoubiquitylated H2B is associated with transcription activation. Like other histone modifications, monoubiquitylation of H2A and H2B is reversible, and is tightly regulated by histone ubiquitin ligases and deubiquitylating enzymes.

Histone ubiquitylation plays a central role in the DNA damage response: RNF8/RNF168 catalyzes K63-linked polyubiquitylation of histone H2A/H2AX and provides a recognition site for RAP80 and other DNA repair proteins. Monoubiquitylation of histones H2A, H2B, and H2AX is also found at the sites of DNA double strand-breaks.

Modifying enimes​

For many years, epigenetic modifications were thought to be irreversible; stable marks propagated through multiple cell divisions. However, research has shown this process to be much more dynamic, and regulated by a specific set of enzymes. These epigenetic regulators can be divided into writers, readers, and erasers.

  • Epigenetic writers
    Enzymes like histone acetyltransferases (HATs), histone methyltransferases (HMTs/KMTs), protein arginine methyltransferases (PRMTs) and kinases are responsible for adding epigenetic marks on histones.
  • Epigenetic readers
    These recognize and bind to the epigenetic marks laid down by writers, thereby determining their functional outcome. They include proteins containing bromodomains, chromodomains and Tudor.
  • Epigenetic erasers
    Erasers, like histone deacetylases (HDACs), lysine demethylases (KDMs) and phosphatases, catalyze the reversal of epigenetic marks.


1.        Greer, E. L. & Shi, Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat. Rev. Genet. 13, 343–57 (2012).

2.        Roth, S. Y., Denu, J. M. & Allis, C. D. Histone acetyltransferases. Annu. Rev. Biochem. 70, 81–120 (2001).

3.        Nowak, S. J. & Corces, V. G. Phosphorylation of histone H3: A balancing act between chromosome condensation and transcriptional activation. Trends Genet. 20, 214–220 (2004).

4.        Rossetto, D., Avvakumov, N. & Côté, J. Histone phosphorylation: A chromatin modification involved in diverse nuclear events. Epigenetics 7, 1098–1108 (2012).

5.        Banerjee, T. & Chakravarti, D. A Peek into the Complex Realm of Histone Phosphorylation. Mol. Cell. Biol. 31, 4858–4873 (2011).

6.        Kschonsak, M. & Haering, C. H. Shaping mitotic chromosomes: From classical concepts to molecular mechanisms. BioEssays 755–766 (2015).

7.        Lowndes, N. F. & Toh, G. W.-L. DNA repair: the importance of phosphorylating histone H2AX. Curr. Biol. 15, R99–R102 (2005).

8.        Pinto, D. M. S. & Flaus, A. Structure and function of histone H2AX. Subcell. Biochem. 50, 55–78 (2010).

9.        Füllgrabe, J., Hajji, N. & Joseph, B. Cracking the death code: apoptosis-related histone modifications. Cell Death Differ. 17, 1238–1243 (2010).

10.      Cao, J. & Yan, Q. Histone ubiquitination and deubiquitination in transcription, DNA damage response, and cancer. Front. Oncol. 2, 26 (2012).

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