Time series data of chromatin and transcription throughout the cell cycle

The occupancy states of DNA-binding nucleosomes and subnucleosome-sized proteins (e.g. transcription factors, replication proteins, etc.) determine the chromatin accessibility landscape and provide additional regulatory context for DNA-templated processes including transcription and DNA replication. Throughout the mitotic cell division cycles, the transcriptome undergoes periodic reprogramming along with replication- and mitosis-induced global chromatin reconfiguration; however, profiling of the cell cycle-specific chromatin dynamics and understandings of its regulatory mechanisms remain limited. Here we employed high-resolution MNase-seq to factor-agnostically map the genome-wide chromatin occupancy with synchronized Saccharomyces cerevisiae cell populations, in parallel with transcriptome profiling by RNA-seq. Throughout the cell cycles, the occupancy of gene-body nucleosomes and promoter subnucleosomes (presumably TFs and polymerase) exhibit both transcription- dependent and independent periodicity, suggesting a decoupling between transcription and chromatin occupancy dynamics. The “phased” positioning of nucleosomes within gene bodies, however, is pervasively disorganized by replication fork progression, and also regulated by the intensity and cell cycle phase of transcriptional activation. Finally, we profiled the chromatin organization around replication origins throughout the complete cell cycle and revealed the chromatin context for origin efficiency.DNA结合核小体（DNA-binding nucleosomes）与亚核小体尺寸蛋白质（subnucleosome-sized proteins）的占用状态，决定了染色质可及性景观（chromatin accessibility landscape），并为转录、DNA复制等以DNA为模板的过程（DNA-templated processes）提供额外的调控背景。在整个有丝分裂细胞分裂周期（mitotic cell division cycles）中，转录组（transcriptome）会伴随复制与有丝分裂诱导的全局染色质重构（replication- and mitosis-induced global chromatin reconfiguration）发生周期性重编程（periodic reprogramming）；然而，针对细胞周期特异性染色质动态（cell cycle-specific chromatin dynamics）的谱型分析，以及对其调控机制（regulatory mechanisms）的认知仍较为有限。本研究利用高分辨率MNase-seq（MNase-seq），结合同步化的酿酒酵母（Saccharomyces cerevisiae）细胞群体，以无因子偏倚的方式绘制全基因组染色质占用图谱，并通过RNA-seq（RNA-seq）并行开展转录组谱型分析。在整个细胞周期中，基因体核小体（gene-body nucleosomes）与启动子亚核小体（promoter subnucleosomes）的占用情况——推测对应转录因子（transcription factors）与聚合酶（polymerase）——同时呈现转录依赖与非依赖的周期性，表明转录与染色质占用动态之间存在解耦现象。然而，基因体内部核小体的“相位性”定位会因复制叉行进（replication fork progression）而广泛紊乱，同时还受转录激活的强度与细胞周期时相的调控。最后，我们对完整细胞周期内复制起点（replication origins）周边的染色质组织进行了谱型分析，揭示了决定复制起点效率（origin efficiency）的染色质环境。