Human Histone Acetyltransferase 1 Protein Preferentially Acetylates H4 Histone Molecules in H3.1-H4 over H3.3-H4

Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA.
Journal of Biological Chemistry (Impact Factor: 4.57). 02/2012; 287(9):6573-81. DOI: 10.1074/jbc.M111.312637
Source: PubMed


In mammalian cells, canonical histone H3 (H3.1) and H3 variant (H3.3) differ by five amino acids and are assembled, along with histone H4, into nucleosomes via distinct nucleosome assembly pathways. H3.1-H4 molecules are assembled by histone chaperone CAF-1 in a replication-coupled process, whereas H3.3-H4 are assembled via HIRA in a replication-independent pathway. Newly synthesized histone H4 is acetylated at lysine 5 and 12 (H4K5,12) by histone acetyltransferase 1 (HAT1). However, it remains unclear whether HAT1 and H4K5,12ac differentially regulate these two nucleosome assembly processes. Here, we show that HAT1 binds and acetylates H4 in H3.1-H4 molecules preferentially over H4 in H3.3-H4. Depletion of Hat1, the catalytic subunit of HAT1 complex, results in reduced H3.1 occupancy at H3.1-enriched genes and reduced association of Importin 4 with H3.1, but not H3.3. Finally, depletion of Hat1 or CAF-1p150 leads to changes in expression of a H3.1-enriched gene. These results indicate that HAT1 differentially impacts nucleosome assembly of H3.1-H4 and H3.3-H4.

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    • "In Drosophila, truncation mutation of the N-terminal tail of H3 compromised replication-coupled nucleosome assembly, indicating that the role of the N-terminal tail of histone H3 in acetylation appears to be conserved among different species [39]. Moreover, H3K56 acetylation is important for nucleosome assembly during DNA replication and repair, both in budding yeast and humans, at least in part by enhancing the interaction between CAF-1 and H3/H4 [51,52,54–56]. "
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    ABSTRACT: Chromatin is subject to proofreading and repair mechanisms during the process of DNA replication, as well as repair to maintain genetic and epigenetic information and genome stability. The dynamic structure of chromatin modulates various nuclear processes, including transcription and replication, by altering the accessibility of the DNA to regulatory factors. Structural changes in chromatin are affected by the chemical modification of histone proteins and DNA, remodeling of nucleosomes, incorporation of variant histones, noncoding RNAs, and nonhistone DNA-binding proteins. Phenotypic diversity and fidelity can be balanced by controlling stochastic switching of chromatin structure and dynamics in response to the environmental disruptors and endogenous stresses. The dynamic chromatin remodeling can, therefore, serve as a sensor, through which environmental and/or metabolic agents can alter gene expression, leading to global cellular changes involving multiple interactive networks. Furthermore its recent evidence also suggests that the epigenetic changes are heritable during the development. This review will discuss the environmental sensing system for chromatin regulation and genetic and epigenetic controls from developmental perspectives.
    01/2014; 5(1). DOI:10.4172/2157-2518.1000156
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    • "These findings indicate that histone H4 also mediate the interaction between H3.3-H4 and their chaperones, raising the possibility that modifications on histone H4 can impact the interactions between histone and H3-H4 binding proteins. Indeed, acetylation of H4K5, K12 by Hat1 in human cells enhances the interactions of importin 4 with H3.1, but not H3.3 (25). In addition, phosphorylation of histone H4S47 increases the interaction between H3.3-H4 and HIRA and consequently regulates H3.3 deposition (26). "
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    ABSTRACT: Phosphorylation of histone H4 serine 47 (H4S47ph) is catalyzed by Pak2, a member of the p21-activated serine/threonine protein kinase (Pak) family and regulates the deposition of histone variant H3.3. However, the phosphatase(s) involved in the regulation of H4S47ph levels was unknown. Here, we show that three phosphatases (PP1α, PP1β and Wip1) regulate H4S47ph levels and H3.3 deposition. Depletion of each of the three phosphatases results in increased H4S47ph levels. Moreover, PP1α, PP1β and Wip1 bind H3-H4 in vitro and in vivo, whereas only PP1α and PP1β, but not Wip1, interact with Pak2 in vivo. These results suggest that PP1α, PP1β and Wip1 regulate the levels of H4S47ph through directly acting on H4S47ph, with PP1α and PP1β also likely regulating the activity of Pak2. Finally, depletion of PP1α, PP1β and Wip1 leads to increased H3.3 occupancy at candidate genes tested, elevated H3.3 deposition and enhanced association of H3.3 with its chaperones HIRA and Daxx. These results reveal a novel role of three phosphatases in chromatin dynamics in mammalian cells.
    Nucleic Acids Research 07/2013; 41(17). DOI:10.1093/nar/gkt583 · 9.11 Impact Factor
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    • "First, it is possible that post-translational modifications on histones H3 and H4, as well as on CAF-1 facilitate (H3-H4)2 release from CAF-1. Supporting this idea, human CAF-1 binds less H3-H4 when H4 is acetylated by the Hat1 complex in vitro, suggesting that acetylation of H4K5 and K12 by Hat1 facilitates the dissociation of H3-H4 from CAF-1 (49). Consistent with this idea, it has been shown that CAF-1 dissociates from replicating DNA prior to deacetylation of H4K5, K12Ac (50). "
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    ABSTRACT: Following acetylation, newly synthesized H3-H4 is directly transferred from the histone chaperone anti-silencing factor 1 (Asf1) to chromatin assembly factor 1 (CAF-1), another histone chaperone that is critical for the deposition of H3-H4 onto replicating DNA. However, it is unknown how CAF-1 binds and delivers H3-H4 to the DNA. Here, we show that CAF-1 binds recombinant H3-H4 with 10- to 20-fold higher affinity than H2A-H2B in vitro, and H3K56Ac increases the binding affinity of CAF-1 toward H3-H4 2-fold. These results provide a quantitative thermodynamic explanation for the specific H3-H4 histone chaperone activity of CAF-1. Surprisingly, H3-H4 exists as a dimer rather than as a canonical tetramer at mid-to-low nanomolar concentrations. A single CAF-1 molecule binds a cross-linked (H3-H4)(2) tetramer, or two H3-H4 dimers that contain mutations at the (H3-H4)(2) tetramerization interface. These results suggest that CAF-1 binds to two H3-H4 dimers in a manner that promotes formation of a (H3-H4)(2) tetramer. Consistent with this idea, we confirm that CAF-1 synchronously binds two H3-H4 dimers derived from two different histone genes in vivo. Together, the data illustrate a clear mechanism for CAF-1-associated H3-H4 chaperone activity in the context of de novo nucleosome (re)assembly following DNA replication.
    Nucleic Acids Research 08/2012; 40(20). DOI:10.1093/nar/gks812 · 9.11 Impact Factor
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