The "Ins and Outs and What-Abouts" of H2A.Z: A tribute to C. David Allis

Abstract

In 2023, the brilliant chromatin biologist C. David Allis passed away leaving a large void in the scientific community and broken hearts in his family and friends. With this review, we want to tribute Dave's enduring inspiration by focusing on the histone variant H2A.Z, a nucleosome component he was the first to discover as hv1 in Tetrahymena. We summarize the latest findings from the past 5 years regarding the mammalian H2A.Z histone, focusing on its deposition and eviction mechanisms, its roles in transcriptional regulation, DNA damage repair, chromatin structure organization, and embryonic development, as well as how its deregulation or mutation(s) of its histone chaperones contribute to disease development. As Dave liked to say 'Every amino acid matters'; the discovery and characterization of functionally different H2A.Z's isoforms, which vary only in three amino acids, prove him-once again-right.

Keywords: C. David Allis; H2A.Z; cancer; chaperones; development; differentiation; gene regulation; oncohistones.

Figure 1

Human H2A.Z isoforms and their intricate “In and Out” mediating complexes. A, “Every amino acid matters”: small amino acid differences in H2A.Z isoforms. Alignment of human H2A.Z.1, H2A.Z.2.1, and H2A.Z.2.2 protein sequences. Identical amino acids are displayed on a white background, while amino acid variations among the H2A.Z isoforms are highlighted in red. PTMs are indicated as follows: acetylation sites are marked as blue circles, methylation as red squares (with one square indicating monomethylation and two squares indicating dimethylation), monoubiquitination as green triangles and SUMOylation as purple pentagons. B, deposition of H2A.Z by EP400 and SRCAP complexes. Depositors of H2A.Z and interacting proteins are illustrated as described in the text. H2A.Z.1 is depicted in dark orange, H2A.Z.2.1 in light orange, unspecified H2A.Z isoform is shown in yellow. H2A.Z.1 is preferentially incorporated in promoter regions and has a serine at position 38; H2A.Z.2.1 is enriched at AT-rich enhancers and has a threonine at position 38. Gene activation is represented by green “+”, and gene silencing is indicated by red “-” circles. Acetylation = blue circles. C, H2A.Z’s novel depositors and well-known evictors with unusual additional functions. SET, DNA-PK, NUTD5, and long noncoding RNAs (lncRNAs) have been identified to (indirectly) mediate H2A.Z chromatin deposition (green arrow).The well-known H2A.Z evictors (red arrow) ANP32E and INO80 show additional buffering and stabilization functions. PTM, posttranslational modifications; ANP32E, acidic nuclear. phosphoprotein 32 family member E; SRCAP, snf2-related CREBBP; DNA-PK, DNA-dependent protein kinase.

Figure 2

H2A.Z regulates various cellular processes. A, H2A.Z in nucleosome dynamics. H2A.Z incorporation influences nucleosome dynamics by increasing DNA accessibility and widening the nucleosomal barrier. This enhanced accessibility facilitates the binding of transcription factors (TF) and has implications for RNA-Pol II dynamics. B, novel findings on acetylation of H2A.Z at regulatory regions. At euchromatic regulatory regions, H2A.Z is acetylated by TIP60, p300, and KAT2A. KAT2A acetylation of H2A.Z.1 at a subset of promoters is licensed by NER pathway proteins XPC-RAD23-CEN2. p300 catalyzed acetylation at enhancers is increased by its direct interaction with H4 acetylation. Blue circles = acetylation. C, H2A.Z’s roles in condensed chromatin. In heterochromatin (HC), H2A.Z is both involved in facultative HC as well as pericentric HC establishment/maintenance. Within facultative HC, H2A.Z.2.1 recruits PRC1 and facilitates H2AK119ub through RING1A. At pericentric HC, H2A.Z occupancy is inhibited by HP1α. CFDP1 interaction is required for proper mitotic spindle formation. Green triangle = monoubiquitination. D, H2A.Z is involved in different DNA repair pathways. H2A.Z/H3.3 nucleosomes increase DNA accessibility for BER pathway proteins and enhance UDG activity to facilitate Uracil excision. At DSBs, H2A.Z recruits Ku80 for NHEJ, and HR pathway proteins through H2A.ZK15ub, which is mediated by RNF168. BER = base excision repair; HR = homologous repair; NHEJ = nonhomologous end joining. Green triangle = monoubiquitination. E, H2A.Z is implicated in DNA replication. H2A.Z licenses ORIs by recruitment of SUV4-20H1 and subsequent dimethylation of H4K20, leading to ORC1 binding. Red squares = methylation. CFDP1, craniofacial development protein 1; PRC1, polycomb repressive complex 1; UDG, uracil DNA glycosylase; ORC1, origin recognition complex subunit 1; ORI, origins of replication; KAT2A, lysine acetyltransferase 2A; NER, nucleotide excision repair.

Figure 3

Deregulation of H2A.Z in cancers. A, overexpression of both H2A.Z isoforms is a hallmark of multiple cancers. Depicted are known cancers with deregulated H2A.Z levels. B, H2A.Z promotes metastatic melanoma. In metastatic melanoma, EP400 and SRCAP complexes, along with their shared subunit YL1, contribute to tumorigenesis by incorporating H2A.Z near E2F1 target genes and by stabilizing acetylation levels of H4 and H2A.Z. Isoliquiritigenin (ISL) has the potential to serve as a therapeutic agent, as it downregulates H2A.Z expression. Gene activation is represented by green “+” circle. Blue circles = acetylation. C, hyperacetylated H2A.Z contributes to tumorigenesis. In both HCC and AML patients, TIP60 is recruited to H2A.Z sites by specific lncRNA or MLL fusion proteins, leading to hyperacetylated H2A.Z-containing nucleosomes and an upregulation of oncogenic target genes. Gene activation is represented by green “+” circle. Blue circles = acetylation. D, H2A.Z supports HDAC inhibitors in the treatment of a certain brain tumor. In DIPG, the presence of H2A.Z is beneficial for cells treated with HDAC inhibitors (HDACi). H2A.Z likely destabilizes nucleosomes containing the oncohistone H3.3K27M through hyperacetylation, facilitating the displacement and degradation of this oncohistone. This process is inhibited by chloroquine treatment. Blue circles = acetylation. DIPG, diffuse intrinsic pontine glioma; E2F1, E2 promoter binding factor 1; AML, acute myeloid leukemia; HDAC, histone deacetylase; SRCAP, snf2-related CREBBP; HCC, hepatocellular carcinoma cell.