Histone acetylation occurs at lysine residues on the amino-terminal tails of the histones (Allfrey and Mirsky, 1964; Phillips, 1963) and it takes place through the antagonistic action of two classes of enzymes, Histone Acetyl Transferases (HATs) and Histone De-Acetylases (HDACs).
It has been recognized for a long time that histone acetylation influences several DNA-related processes including DNA replication, repair and transcription. Specifically, it is well-known that acetylation of histone tails exerts a role on transcription and that a positive correlation exists between transcription of a gene and histone acetylation at its promoter (Allfrey et al., 1964; Dion et al., 2005). In higher eukaryotic cells, conditions that lead to massive perturbations of gene expression, like developmental cues and cancer, are accompanied by modifications in the histone acetylation pattern on enhancers and promoters (Gong et al., 2016; Kinnaird et al., 2016; Podobinska et al., 2017). In yeast, variation of growing conditions and environmental stress induce changes in gene expression that go together with alterations in the histone acetylation state of gene promoters (Kuang et al., 2014; Weiner et al., 2015). It has been proposed that the histone acetylation levels are a sensor of the metabolic state of the cell. Indeed, metabolism changes the cellular concentration of acetyl-coenzyme A (Acetil-CoA) the donator of acetyl groups for HATs. Furthermore, in the cell NAD+
levels increase when cellular nutrient levels are low and this activates some HDACs (like the sirtuins) that deacetylate various proteins including histones (Yu and Auwerx, 2009).
Histone acetylation has been proposed to promote transcription through two different non-exclusive mechanisms. (1) Acetylated proteins, including histones, are recognized and bound by specific protein domains called bromodomains (Dhalluin et al., 1999). Proteins containing bromodomains are the readers of the acetylation mark. So far, in yeast 8 proteins containing bromodomains have been identified (Gcn5, Snf2, Spt7, Sth1, Rsc1, Rsc2, Bdf1, Bdf2). Significantly, all these proteins are nuclear proteins having a positive role in transcription regulation (Josling et al., 2012). Recently, another
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protein domain, the YEATS (Yaf9, ENL, AF9, Taf14 and Sas5) domain, has been identified as an acetyl reader specific for acetylated Lys9 of histone H3, expanding so the putative number of histone acetylation readers (Li et al., 2014). (2) Acetylation of lysines on histone tails neutralize the positive charge of histones decreasing their affinity for DNA and disfavoring so chromatin organization in secondary and tertiary structures and making the DNA more accessible to the binding of TFs, members of the PIC or other transcriptional co-activators that do not contain bromodomains (Garcia-Ramirez et al., 1995; Wang and Hayes, 2008) (Figure 8). However, the importance of histone acetylation for transcription activation and PIC assembly is still very controversial and among the limited number of proteins containing bromodomains identified so far in yeast only one, Sth1, is essential (Bdf1 and Bdf2 deletions are synthetically lethal). Furthermore, evidence of the in vivo role of histone acetylation in chromatin de-compaction are still missing.
Figure 8. Histone acetylation and transcription (Verdin and Ott, 2015).
HATs, the writers
HATs are the enzymes that acetylate the histone tails. They belong to the big class of Lysine Acetyl Transferases (KATs) and indeed many of them acetylate also non-histone proteins, among these many TFs and other nuclear proteins, but also some cytoplasmic or mitochondrial proteins. HATs are structurally characterized by a central catalytic core, where acetyl-CoA finds place, flanked by
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terminal and C–terminal regions important for histone or substrate binding and specificity. Indeed, HATs have a strong specificity for specific lysine residues on histone tails. HATs are classified in three main families (GNAT, MYST and orphan) depending on the structure of the catalytic core and the catalytic mechanism of action (Yuan and Marmorstein, 2013).
GNATs (Gcn5-related N-acetyltransferases) are a family of HATs that includes Gcn5, PCAF (p300/CBP-associated factor), Elp3, Hat1, Hpa2 and Nut1. The catalytic core of GNATs is characterized by a short (160 residues) highly conserved motif, named motif A, important for Acetyl-CoA binding. Many GNATs have also a C-terminal bromodomain. The catalytic mechanism of acetylation involves the formation of a ternary complex between the HAT, the histone and a molecule of Acetyl-CoA. A conserved glutamic acid residue in the motif A (E173 for Gcn5) is crucial for the reaction (Marmorstein and Trievel, 2009).
The MYST family of HATs comprises the human MOZ (Sas3 in yeast), Ybf2, Sas2, Tip60/Esa1 and the human MORF and HBO1. They are characterized by the presence of cysteine-rich zinc finger domains important for HAT activity and N-terminal chromodomains. The catalytic core is longer than the GNAT one (around 250 residues). Furthermore, some also have the motif A typical of GNATs. They acetylate histones through a “ping-pong” mechanism (see below) where a cysteine residue of the HAT is acetylated first and then it transfers the acetyl group to a lysine residue on the histone tail (Marmorstein and Trievel, 2009).
All the HATs that do not belong to the GNAT and the MYST families made up the family of orphan HATs such as p300/CBP and Rtt109. They are characterized by structural heterogeneity and by the presence of a big HAT catalytic domain (up to 500 residues for the human p300/CBP). The heterogeneity of structural domains in the catalytic core reflects also different catalytic mechanisms.
The most studied one is the “hit and run” mechanism of p300/CBP (Liu et al., 2008).
32 HDACs, the erasers
HDAC are the enzymes that remove the acetyl group from histone tails. Similarly to HATs, also HDACs are able to de-acetylate also non-histone proteins. Contrary to HATs, HDACs are characterized by a lower level of substrate specificity and some of them are redundant among each other. They are classified in three main groups. Group I (Rpd3/ HDAC1, Hos1, Hos2) and Group II (Hda1, Hos3) are all Zinc-dependent, while group III are NAD+ dependent. Sirtuins, among the most studied HDAC in both yeast and human, belong to group III. Sir2, Hst1 and Hst2 de-acetylate both histones and non-histone proteins, while Hst3 and Hst4 de-acetylate specifically H3K56 (de Ruijter et al., 2003).