The Histone Variant H2A.Z C-terminal Domain Has Locus- Specific Differential Effects on H2A.Z Occupancy and Nucleosome Localization

The incorporation of histone variant H2A.Z, a conserved H2A variant, into nucleosomes creates specialized chromatin domains that regulate DNA-templated processes, including transcription. H2A.Z-containing nucleosomes may poise gene regulatory regions for transcription, but mechanistic details are lacking. In Saccharomyces cerevisiae, the diverging H2A.Z C-terminus is thought to provide the H2A.Z exclusive functions. To elucidate the roles of this H2A.Z C-terminus genome wide, we made use of derivatives where the C-terminus was replaced with the corresponding region of H2A (ZA protein), or the H2A region plus a transcriptional activating peptide, with the idea of regenerating the H2A.Z-dependent regulation globally. An assessment of the genome-wide distribution of these H2A.Z derivatives shows that the H2A.Z C-terminal region is crucial for both maintaining the occupation level of H2A.Z and the proper positioning of the targeted nucleosomes. Interestingly, the specific contribution on incorporation efficiency vs nucleosome positioning varies enormously, depending on loci analyzed. For the ZA protein, positioning changes most importantly near origins of replication and snoRNA gene promoters, while incorporation is affected on all other sites. Furthermore, the role of H2A.Z in global transcription regulation also depends on its C-terminal region. Remarkably however, the latter mostly involves genes without a H2A.Z nucleosome in the promoter.组蛋白变体H2A.Z（histone variant H2A.Z）是一类保守的H2A变体，将其掺入核小体可形成特化的染色质结构域，进而调控以DNA为模板的各类生物学过程，包括转录。含有H2A.Z的核小体能够使基因调控区域处于转录就绪状态，但相关的分子机制细节仍有待阐明。在酿酒酵母（Saccharomyces cerevisiae）中，学界普遍认为分化的H2A.Z C端结构域负责介导H2A.Z独有的生物学功能。为了在全基因组层面解析H2A.Z C端的具体作用，我们构建了两类H2A.Z衍生物：一类是将H2A.Z的C端替换为H2A的对应区域（即ZA蛋白（ZA protein）），另一类则是将H2A.Z的C端替换为H2A区域外加一段转录激活肽，以期在全局范围内重建依赖H2A.Z的基因调控过程。对这些H2A.Z衍生物的全基因组分布进行检测后发现，H2A.Z C端区域对维持H2A.Z的核小体占据水平，以及靶核小体的正确定位均发挥关键作用。值得注意的是，其对核小体整合效率与定位的具体调控效应，因所分析的基因座不同而呈现出显著差异。对于ZA蛋白而言，核小体定位的改变主要集中在复制起点与核仁小RNA（snoRNA）基因启动子区域，而H2A.Z的整合效率则在其余所有位点受到影响。此外，H2A.Z在全局转录调控中的功能同样依赖于其C端结构域。然而令人意外的是，这类调控大多作用于启动子中不含H2A.Z核小体的基因。