Plot Data for S10 Fig.

The variant histone H2A.Z is deposited into nucleosomes immediately downstream of promoters, where it plays a critical role in transcription. The site-specific deposition of H2A.Z is catalyzed by the SWR complex, a conserved chromatin remodeler with affinity for promoter-proximal nucleosome-depleted regions (NDRs) and histone acetylation. By comparing the genomic distribution of H2A.Z in wild-type and SWR-deficient cells, we found that SWR is also responsible for depositing H2A.Z at thousands of non-canonical sites not directly linked to NDRs or histone acetylation. To understand the targeting mechanism of H2A.Z, we presented SWR to a library of canonical nucleosomes isolated from yeast and analyzed the preferred substrates. Our results revealed that SWR preferentially deposited H2A.Z into a subset of endogenous H2A.Z sites, which are overrepresented by polyadenine tracts on the top strands of the DNA duplex at the nucleosomal entry-exit sites. Insertion of polyadenine sequences into recombinant nucleosomes near the outgoing H2A-H2B dimer enhanced SWR’s affinity for the nucleosomal substrate and increased its H2A.Z insertion activity. These findings suggest that the genome encodes sequence-based information that facilitates remodeler-mediated targeting of H2A.Z.

变体组蛋白H2A.Z被沉积于启动子下游紧邻的核小体中，在转录过程中发挥关键调控作用。H2A.Z的位点特异性沉积由SWR复合物（SWR complex）催化，该复合物是一类保守的染色质重塑因子（chromatin remodeler），对启动子近端核小体缺失区域（nucleosome-depleted regions, NDRs）与组蛋白乙酰化位点具有结合亲和力。通过比较野生型与SWR缺陷细胞中H2A.Z的基因组分布，我们发现SWR还负责在数千个与NDRs或组蛋白乙酰化无直接关联的非经典位点沉积H2A.Z。为阐明H2A.Z的靶向定位机制，我们将SWR作用于从酵母中分离的经典核小体文库，并分析其优先结合的底物。研究结果显示，SWR优先将H2A.Z沉积到一类内源性H2A.Z位点中，这些位点在DNA双链的核小体进出位点的正链上富含多聚腺嘌呤序列（polyadenine tracts）。将多聚腺嘌呤序列插入重组核小体中靠近即将解离的H2A-H2B二聚体的区域，可增强SWR对核小体底物的亲和力，并提升其H2A.Z插入活性。上述发现表明，基因组编码了基于序列的信息，可促进重塑因子介导的H2A.Z靶向定位。