Acetylation is one of the most widely studied histone modifications since it was one of the first discovered to influence transcriptional regulation. Unmodified lysine residues are positively charged but acetylation results in neutralization of the charge on histones, which reduces the interaction of histones and negatively charged DNA. The charge neutralization results in a weaker histone: DNA interaction, allows transcription factor binding and significantly increases gene expression.

Histone acetylation is involved in cell cycle regulation, cell proliferation, and apoptosis and may play a vital role in regulating many other cellular processes, including cellular differentiation, DNA replication and repair, nuclear import and neuronal repression. An imbalance in the equilibrium of histone acetylation is associated with tumorigenesis and cancer progression.

Enzymatic regulation

Acetyl groups are added to lysine residues of histones H3 and H4 by histone acetyltransferases (HAT) and removed by deacetylases (HDAC). Histone acetylation is largely targeted to promoter regions, known as promoter-localized acetylation. For example, acetylation of K9 and K27 on histone H3 (H3K9ac and H3K27ac) is usually associated with enhancers and promoters of active genes. Low levels of global acetylation are also found throughout transcribed genes, whose function remains unclear.

Methylation is added to the lysine or arginine residues of histones H3 and H4, with different impacts on transcription. Arginine methylation promotes transcriptional activation while lysine methylation is implicated in both transcriptional activation and repression depending on the methylation site. This flexibility may be explained by the fact that that methylation does not alter histone charge or directly impact histone-DNA interactions, unlike acetylation.

Lysines can be mono-, di-, or tri-methylated, providing further functional diversity to each site of methylation. For example, both mono- and tri-methylation on K4 of histone H3 (H3K4me1and H3K4me3) are activation markers, but with unique nuances: H3K4me1 typically marks transcriptional enhancers, while H3K4me3 marks gene promoters. Meanwhile, tri-methylation of K36 (H3K36me3) is an activation marker associated with transcribed regions in gene bodies.

In contrast, tri-methylation on K9 and K27 of histone H3 (H3K9me3 and H3K27me3) are repressive signals with unique functions: H3K27me3 is a temporary signal at promoter regions that controls development regulators in embryonic stem cells, including Hox and Sox genes. Meanwhile, H3K9me3 is a permanent signal for heterochromatin formation in gene-poor chromosomal regions with tandem repeat structures, 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.

Enzymatic regulation

Histone methylation is a stable mark propagated through multiple cell divisions, and for many years was thought to be irreversible. However, it was recently discovered to be an actively regulated and reversible process.

Methylation: histone methyltransferases (HMTs)

• Lysine
• SET domain-containing (histone tails)
• Non-SET domain-containing (histone cores)
• Arginine
• PRMT (protein arginine methyltransferases) family

Demethylation: histone demethylases

• Lysine
• KDM1/LSD1 (lysine-specific demethylase 1)
• JmjC (Jumonji domain-containing)
• Arginine
• PAD4/PADI4

Histone phosphorylation is a critical intermediate step in chromosome condensation during cell division, transcriptional regulation, and DNA damage repair. Unlike acetylation and methylation, histone phosphorylation establishes interactions between other histone modifications and serves as a platform for effector proteins, which leads to a downstream cascade of events.

Phosphorylation occurs on all core histones, with differential effects on each. Phosphorylation of histone H3 at serine 10 and 28, and histone H2A on T120, are involved in chromatin compaction and the regulation of chromatin structure and function during mitosis. These are important markers of cell cycle and cell growth that are conserved throughout eukaryotes. Phosphorylation of H2AX at S139 (resulting in γH2AX) serves as a recruiting point for DNA damage repair proteins and is one of the earliest events to occur after DNA double-strand breaks. H2B phosphorylation is not as well studies but is found to facilitate apoptosis-related chromatin condensation, DNA fragmentation, and cell death.

All histone core proteins can be ubiquitylated, but H2A and H2B are most commonly and are two of the most highly ubiquitylated proteins in the nucleus. Histone ubiquitylation plays a central role in the DNA damage response.

Monoubiquitylation of histones H2A, H2B, and H2AX is found at sites of DNA double-strand breaks. The most common forms are monoubiquitylated H2A on K119 and H2B on K123 (yeast)/K120 (vertebrates). Monoubiquitylated H2A is also associated with gene silencing, whereas H2B is also associated with transcription activation

Poly-ubiquitylation is less common but is also important in DNA repair-- polyubiquitylation of H2A and H2AX on K63 provides a recognition site for DNA repair proteins, like RAP80.

Enzymatic regulation

Like other histone modifications, monoubiquitylation of H2A and H2B is reversible and is tightly regulated by histone ubiquitin ligases and deubiquitylating enzymes.

Monoubiquitylation

• H2A: polycomb group proteins
• H2B: Bre1 (yeast) and its homologs RNF20/RNF40 (mammals)

Polyubiquitylation

• H2A/H2AX K63: RNF8/RNF168

References

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