The histone variant H2A.Z in gene regulation

Abstract

The histone variant H2A.Z is involved in several processes such as transcriptional control, DNA repair, regulation of centromeric heterochromatin and, not surprisingly, is implicated in diseases such as cancer. Here, we review the recent developments on H2A.Z focusing on its role in transcriptional activation and repression. H2A.Z, as a replication-independent histone, has been studied in several model organisms and inducible mammalian model systems. Its loading machinery and several modifying enzymes have been recently identified, and some of the long-standing discrepancies in transcriptional activation and/or repression are about to be resolved. The buffering functions of H2A.Z, as supported by genome-wide localization and analyzed in several dynamic systems, are an excellent example of transcriptional control. Posttranslational modifications such as acetylation and ubiquitination of H2A.Z, as well as its specific binding partners, are in our view central players in the control of gene expression. Understanding the key-mechanisms in either turnover or stabilization of H2A.Z-containing nucleosomes as well as defining the H2A.Z interactome will pave the way for therapeutic applications in the future.

Keywords: CRISPR/Cas9; Domino; H2A.Z; H2Av; Histone variant; Tip60; p400.

Fig. 1

Schematic representation of the different human H2A.Z isoforms. Alignment of H2A.Z.1, H2A.Z.2.1 and H2A.Z.2.2 protein sequences. Highlighted in gray are residues that differ between H2A.Z.1 and H2A.Z.2.1, while residues highlighted in yellow are the ones not conserved between H2A.Z.2.1 and H2A.Z.2.2. Yellow, red, blue, pink and green balls indicate sites of acetylation, methylation, phosphorylation, SUMOylation and ubiquitination, respectively. Please look at Table 2 for more details about the PTMs of H2A.Z

Fig. 2

Mechanisms of recruitment of the Ep400/Tip60 complex. The Ep400/Tip60 complex, involved in loading and acetylation of the histone variant H2A.Z, can be recruited to its target genomic sites via interactions with a transcription factors (TFs) or b subunits of the pre-initiation complex (PIC) composed of general transcription factors (GTF; TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) and RNA polymerase II (RNAPII). In addition, the Ep400/Tip60 complex can be recruited to its target genomic sites via interactions with posttranslationally modified histone proteins, for example: c MRG15 binds to H3K4me1 or H3K4me3 [122], while Tip60 binds to H3K4me1 via its chromodomain [118]. d GAS41 binds to H3K14ac, H3K27ac or H3K122suc using its YEAST domain [–127]. For simplicity reasons, only the Ep400/Tip60 complex is shown; however, similar mechanisms of recruitment can be used by the SRCAP complex. TFBS transcription factor binding site

Fig. 3

Regulation of H2A.Z and its involvement in transcription. Two examples are used to explain the function of H2A.Z in gene regulation: a the case of the androgen system focusing on the PSA locus and b the case of the estrogen system focusing on the TFF1 locus. a In a repressed or poised (OFF) state, the H2A.Z-specific loading machineries are recruited to the PSA locus via not well-defined mechanisms that may involve TFs and/or histone modifications. In this scenario, H2A.Z is deposited by SRCAP and/or p400/Tip60 complexes [119, 122] and the deacetylation and ubiquitination machineries are probably recruited via interactions with DNA binding proteins and/or posttranslationally modified histones (not depicted in the figure). The deacetylation machinery removes the acetylation mark from H2A.Z, which is instead ubiquitinated on its C-terminus by E3 ubiquitin ligases (we speculate that RING1B is involved in the AR signaling cascade [58, 145]). Upon gene activation (ON), deubiquitination (for example, USP10 [51]) and loading/acetylation/deubiquitination machineries are recruited/stabilized via interactions with the Androgen Receptor (AR) that binds to its cognate sequences (androgen receptor-binding element, ARE) and/or histone modifications [119, 122]. This leads to H2A.Z deubiquitination [52] and acetylation [59, 122] finally leading to gene activation which is associated with reduced H2A.Z occupancy [51, 52]. b In a repressed (OFF) state, FoxA1 binds to the distal FoxA1-binding site (FBS) of the TFF1 locus where it recruits the p400/Tip60 complex that supports loading of H2A.Z. In this state, H2A.Z is poorly enriched at the TFF1 promoter and, as consequence, nucleosome occupancy is poorly defined [50]. Upon gene induction, the estrogen receptor α (ERα) binds to its cognate sequence (estrogen receptor-binding element, ERE) where it recruits the p400/Tip60 complex leading to loading of H2A.Z at the promoter and as consequence increased nucleosome positioning and finally to gene activation. At the same time, H2A.Z enrichment at the FBS is reduced [50]

Fig. 4

Summary of the different possible strategies that can be employed to deplete a histone gene via the CRISPR/Cas9 technology. A protein-coding gene can be targeted on its 5′-UTR leading to mRNA destabilization or preventing its translation. Alternatively, the ORF can be targeted, leading to the formation of a premature STOP codon. Finally, targeting of the 3′-UTR can lead to mRNA destabilization or to a translational block but it can also increase the mRNA stability or the translation efficiency. UTR untranslated region, ORF open reading frame