Histone acetyltransferases (HATs) are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl-CoA to form ε-N-acetyllysine. DNA is wrapped around histones, and, by transferring an acetyl group to the histones, genes can be turned on and off. In general, histone acetylation increases gene expression.
In general, histone acetylation is linked to transcriptional activation and associated with euchromatin. Euchromatin, which is less densely compact, allows transcription factors to bind more easily to regulatory sites on DNA, causing transcriptional activation. When it was first discovered, it was thought that acetylation of lysine neutralizes the positive charge normally present, thus reducing affinity between histone and (negatively charged) DNA, which renders DNA more accessible to transcription factors. Research has emerged, since, to show that lysine acetylation and other posttranslational modifications of histones generate binding sites for specific protein–protein interaction domains, such as the acetyllysine-binding bromodomain. Histone acetyltransferases can also acetylate non-histone proteins, such as nuclear receptors and other transcription factors to facilitate gene expression.
HAT families
HATs are traditionally divided into two different classes based on their subcellular localization. They contain a bromodomain, which helps them recognize and bind to acetylated lysine residues on histone substrates. Gcn5, p300/CBP, and TAF<sub>II</sub>250 are some examples of type A HATs that cooperate with activators to enhance transcription. Type B HATs are located in the cytoplasm and are responsible for acetylating newly synthesized histones prior to their assembly into nucleosomes. These HATs lack a bromodomain, as their targets are unacetylated. The acetyl groups added by type B HATs to the histones are removed by HDACs once they enter the nucleus and are incorporated into chromatin. Hat1 is one of the few known examples of a type B HAT.
thumbnail|Relative sizes and locations of important domains for representative HATs (HAT = catalytic acetyltransferase domain; Bromo = bromodomain; Chromo = chromodomain; Zn = zinc finger domain). The number of amino acid residues in each HAT is indicated at the right in each example.
Gcn5-related N-acetyltransferases (GNATs)
HATs can be grouped into several different families based on sequence homology as well as shared structural features and functional roles. The Gcn5-related N-acetyltransferase (GNAT) family includes Gcn5, PCAF, Hat1, Elp3, Hpa2, Hpa3, ATF-2, and Nut1. These HATs are generally characterized by the presence of a bromodomain, and they are found to acetylate lysine residues on histones H2B, H3, and H4. Tip60 (Tat-interactive protein, 60 kDa) was the first human MYST family member to exhibit HAT activity. Sas3 found in yeast is a homolog of MOZ (monocytic leukemia zinc finger protein), which is an oncogene found in humans. Esa1 was the first essential HAT to be found in yeast, and MOF is its homolog in fruit flies. The HAT activity of the latter is required for the twofold increased transcription of the male X chromosome (dosage compensation) in flies. Human HBO1 (HAT bound to ORC1) was the first HAT shown to associate with components of the origin of replication complex. MORF (MOZ-related factor) exhibits very close homology to MOZ throughout its entire length. and contain several zinc finger regions, a bromodomain, a catalytic (HAT) domain, and regions that interact with other transcription factors. and it is required for p300/CBP to function in transcriptional activation. Rtt109 is a fungal-specific HAT that requires association with histone chaperone proteins for activity.
Nuclear receptor coactivators
Three important nuclear receptor coactivators that display HAT activity are SRC-1, ACTR, and TIF-2. Human SRC-1 (steroid receptor coactivator-1) is known to interact with p300/CBP and PCAF, and its HAT domain is located in its C-terminal region. ACTR (also known as RAC3, AIB1, and TRAM-1 in humans) shares significant sequence homology with SRC-1, in particular in the N-terminal and C-terminal (HAT) regions as well as in the receptor and coactivator interaction domains.
{| class="wikitable" border="3" style="text-align: center; "
|-
!Family
! Members !! Organism !! Associated complexes !! Substrate specificity !! Structural features
|-
| rowspan="10" |GNAT
| Gcn5 || S. cerevisiae || SAGA, SLIK (SALSA), ADA,
HAT-A2
| H2B, H3, (H4) || Bromodomain
|-
| GCN5 || D. melanogaster || SAGA, ATAC || H3, H4 || Bromodomain
|-
| GCN5 || H. sapiens || STAGA, TFTC || H3, (H4, H2B) || Bromodomain
|-
| PCAF || H. sapiens || PCAF || H3, H4 || Bromodomain
|-
| Hat1 || S. cerevisiae<br/>H. sapiens|| HAT-B, NuB4, HAT-A3 || H4, (H2A) ||
|-
| Elp3 || S. cerevisiae || Elongator || H3, H4, (H2A, H2B) ||
|-
| Hpa2 || S. cerevisiae || HAT-B || H3, H4 ||
|-
| Hpa3 || S. cerevisiae || || H3, H4 ||
|-
| ATF-2 || S. cerevisiae<br/>H. sapiens|| || H2B, H4 ||
|-
| Nut1 || S. cerevisiae || Mediator || H3, H4 ||
|-
| rowspan="8" |MYST
| Esa1 || S. cerevisiae || NuA4, piccolo NuA4|| H2A, H4, (H2B, H3) || Chromodomain
|-
| Sas2 || S. cerevisiae || SAS, NuA4|| H4, (H2A, H3) ||
|-
| Sas3 (Ybf2) || S. cerevisiae || NuA3 || H3, (H4, H2A) ||
|-
| Tip60 || H. sapiens || Tip60, NuA4|| H2A, H4, (H3) || Chromodomain
|-
| MOF || D. melanogaster || MSL || H4, (H2A, H3) || Chromodomain
|-
| MOZ || H. sapiens || MSL || H3, H4 ||
|-
| MORF || H. sapiens || MSL || H3, H4 ||
|-
| HBO1 || H. sapiens || ORC || H3, H4 ||
|-
| rowspan="2" |p300/CBP
| p300 || H. sapiens || || H2A, H2B, H3, H4 || Bromodomain
|-
| CBP || H. sapiens || || H2A, H2B, H3, H4 || Bromodomain
|-
| rowspan="3" |SRC
(nuclear receptor coactivators)
| SRC-1 || H. sapiens || ACTR/SRC-1 || H3, H4 ||
|-
| ACTR (RAC3, AIB1, TRAM-1, SRC-3) || H. sapiens || ACTR/SRC-1 || H3, H4 ||
|-
| TIF-2 (GRIP1) || H. sapiens || || H3, H4 ||
|-
| rowspan="4" |Other
| TAF<sub>II</sub>250 (TAF1) || S. cerevisiae<br/>H. sapiens|| TFIID || H3, H4, (H2A) || Bromodomain
|-
| TFIIIC (p220, p110, p90) || H. sapiens || TFIIIC || H2A, H3, H4 ||
|-
| Rtt109 || S. cerevisiae || Histone chaperones || H3 ||
|-
| CLOCK || H. sapiens || || H3, H4 ||
|}
Overall structure
thumbnail|Crystal structure of Tetrahymena Gcn5 with bound coenzyme A and histone H3 peptide (PDB 1QSN). The central core (green), flanking N- and C-terminal segments (blue), coenzyme A (orange), and histone peptide (red) are shown.
In general, HATs are characterized by a structurally conserved core region made up of a three-stranded β-sheet followed by a long α-helix parallel to and spanning one side of it. The first part of the reaction involves the formation of a covalent intermediate in which a cysteine residue becomes acetylated following nucleophilic attack of this residue on the carbonyl carbon of acetyl-CoA. Then, a glutamate residue acts as a general base to facilitate transfer of the acetyl group from the cysteine to the histone substrate in a manner analogous to the mechanism used by GNATs. When Esa1 is assembled in the piccolo NuA4 complex, it loses its dependence on the cysteine residue for catalysis, which suggests that the reaction may proceed via a ternary bi-bi mechanism when the enzyme is part of a physiologically relevant multiprotein complex.
p300/CBP family
In human p300, Tyr1467 acts as a general acid and Trp1436 helps orient the target lysine residue of the histone substrate into the active site.
Lysine selectivity
Different HATs, usually in the context of multisubunit complexes, have been shown to acetylate specific lysine residues in histones.
GNAT family
Gcn5 cannot acetylate nucleosomal histones in the absence of other protein factors. PCAF has also been observed to acetylate c-MYC, GATA-2, retinoblastoma (Rb), Ku70, and E1A adenovirus protein. It can also autoacetylate, which facilitates intramolecular interactions with its bromodomain that may be involved in the regulation of its HAT activity. E1A adenovirus protein, and S-HDAg (hepatitis delta virus small delta antigen). Acetylation of yeast Rtt109 at Lys290 is also required for it to exhibit full catalytic activity. Some HATs are also inhibited by acetylation. For example, the HAT activity of the nuclear receptor coactivator ACTR is inhibited upon acetylation by p300/CBP. Chromatin in the cell can be found in two states: condensed and uncondensed. The latter, known as euchromatin, is transcriptionally active, whereas the former, known as heterochromatin, is transcriptionally inactive. Histones comprise the protein portion of chromatin. There are five different histone proteins: H1, H2A, H2B, H3, and H4. A core histone is formed when two of each histone subtype, excluding H1, form a quaternary complex. This octameric complex, in association with the 147 base pairs of DNA coiled around it, forms the nucleosome. Histone H1 locks the nucleosome complex together, and it is the last protein to bind in the complex.
Histones tend to be positively charged proteins with N-terminal tails that stem from the core. The phosphodiester backbone of DNA is negative, which allows for strong ionic interactions between histone proteins and DNA. Histone acetyltransferases transfer an acetyl group to specific lysine residues on histones, which neutralizes their positive charge and thus reduces the strong interactions between the histone and DNA. In addition, some histone modifications are associated with both enhanced and repressed activity, in a context-dependent manner.
HATs act as transcriptional co-activators or gene silencers and are most often found in large complexes made up of 10 to 20 subunits, some of which shared among different HAT complexes.
Clinical significance
The ability of histone acetyltransferases to manipulate chromatin structure and lay an epigenetic framework makes them essential in cell maintenance and survival. The process of chromatin remodeling involves several enzymes, including HATs, that assist in the reformation of nucleosomes and are required for DNA damage repair systems to function. HATs have been implicated as accessories to disease progression, specifically in neurodegenerative disorders. For instance, Huntington's disease is a disease that affects motor skills and mental abilities. The only known mutation that has been implicated in the disease is in the N-terminal region of the protein huntingtin (htt). It has been reported that htt directly interacts with HATs and represses the catalytic activity of p300/CBP and PCAF in vitro.
The human premature aging syndrome Hutchinson Gilford progeria is caused by a mutational defect in the processing of lamin A, a nuclear matrix protein. In a mouse model of this condition, recruitment of repair proteins to sites of DNA damage is delayed. The molecular mechanism underlying this delayed repair response involves a histone acetylation defect. Specifically, histone H4 is hypoacetylated at a lysine 16 residue (H4K16) and this defect is due to reduced association of histone acetyltransferase, Mof, to the nuclear matrix
HATs have also been associated with control of learning and memory functions. Studies have shown that mice without PCAF or CBP display evidence of neurodegeneration.
The misregulation of the equilibrium between acetylation and deacetylation has also been associated with the manifestation of certain cancers. If histone acetyltransferases are inhibited, then damaged DNA may not be repaired, eventually leading to cell death. Controlling the chromatin remodeling process within cancer cells may provide a novel drug target for cancer research. Attacking these enzymes within cancer cells could lead to increased apoptosis due to high accumulation of DNA damage. One such inhibitor of histone acetyltransferases is called garcinol. This compound is found within the rinds of the garcinia indica fruit, otherwise known as mangosteen. To explore the effects of garcinol on histone acetyltransferases, researchers used HeLa cells. The cells underwent irradiation, creating double-strand breaks within the DNA, and garcinol was introduced into the cells to see if it influenced the DNA damage response. If garcinol is successful at inhibiting the process of non-homologous end joining, a DNA repair mechanism that shows preference in fixing double-strand breaks, then it may serve as a radiosensitizer, a molecule that increases the sensitivity of cells to radiation damage. Increases in radiosensitivity may increase the effectiveness of radiotherapy.