The histone variant H2A.Z in yeast is almost exclusively incorporated into the +1 nucleosome in the direction of transcription

To investigate the incorporation dynamics of histone variant H2A.Z, we determined its genomic localization at single nucleosome resolution, as well as the localization of its chromatin remodelers Swr1 and Ino80. We find that Swr1 binding alone is a poor predictor of H2A.Z occupancy levels, and that normal Swr1 and Ino80 localization are actually dependent on H2A.Z. Additionally, we find that H2A.Z's bimodal incorporation on either side of the NDR is not a general feature of TSS, but is specifically a marker for bidirectional transcription, such that the upstream flanking -1 H2A.Z-containing nucleosome is more appropriately considered as a +1 H2A.Z nucleosome for antisense transcription. Overall design: MNase-ChIP-seq data was produced to determine at single nucleotide resolution the genomic localization of the histone variant H2A.Z. ChIP-seq was performed to determine the genomic localization of chromatin remodelers Ino80 and Swr1 both in the presence and absence of histone variant H2A.Z. Smore-seq was performed with both ribo depletion and poly-A selection to map transcripts across the genome.

为探究组蛋白变体H2A.Z（histone variant H2A.Z）的整合动力学，本研究在单核小体分辨率下测定了其基因组定位，并同时确定了其染色质重塑因子Swr1与Ino80的定位。本研究发现，仅依靠Swr1的结合无法有效预测H2A.Z的占据水平，且正常状态下Swr1与Ino80的定位实际上依赖于H2A.Z的存在。此外，我们观察到H2A.Z在核小体缺失区（nucleosome-depleted region, NDR）两侧的双峰整合模式并非转录起始位点（transcription start site, TSS）的通用特征，而是双向转录的特异性标记；据此，对于反义转录而言，上游侧翼的-1位含H2A.Z核小体，更适宜被归类为反义转录的+1位H2A.Z核小体。实验整体设计：通过微球菌核酸酶染色质免疫共沉淀测序（MNase-ChIP-seq），以单核苷酸分辨率测定组蛋白变体H2A.Z的基因组定位；通过染色质免疫共沉淀测序（ChIP-seq），分别在存在与缺失组蛋白变体H2A.Z的两种条件下，测定染色质重塑因子Ino80与Swr1的基因组定位；同时采用核糖体RNA去除（ribo depletion）与polyA尾富集（poly-A selection）两种文库构建策略开展Smore-seq测序，以绘制全基因组转录本的定位图谱。