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. Overall design: Time course of yeast released from a-factor and collected every 10 min from T=0 min (prior to release) to 150 min (Replicate 1) or 140 min (Replicate 2) post release. Because the recovery time from a-factor arrest for Replicate 1 is about one time point longer than Replicate 2, T=10 min for Replicate 1 is discarded and all later time points are shifted one time point earlier when aligning the cell cycle timeline with Replicate 2. Two biological replicates are conducted which include 30 samples of MNase chromatin and 29 samples of RNA (T=110 min for Replicate 2 is of bad quality and discarded).

DNA结合核小体与亚核小体尺寸蛋白（如转录因子、复制蛋白等）的占据状态，决定了染色质可及性图谱，并为转录、DNA复制等以DNA为模板的生物学过程提供额外的调控背景。在整个有丝分裂细胞周期中，转录组会伴随复制及有丝分裂诱导的全局染色质重构型发生周期性重编程；然而，针对细胞周期特异性染色质动态的解析以及对其调控机制的认知仍较为有限。本研究采用高分辨率微球菌核酸酶测序（MNase-seq），结合同步化的酿酒酵母（Saccharomyces cerevisiae）细胞群体，以因子不偏倚的方式绘制全基因组染色质占据图谱，同时通过RNA测序（RNA-seq）开展转录组分析。在整个细胞周期中，基因体核小体与启动子亚核小体（推测对应转录因子与聚合酶）的占据情况同时表现出转录依赖与非依赖的周期性，提示转录与染色质占据动态之间存在解偶联现象。然而，基因体内核小体的相位性（phased）定位会普遍因复制叉行进而发生紊乱，同时还受转录激活的强度与细胞周期时相调控。最后，本研究对完整细胞周期内复制起始位点周围的染色质组织进行了全景分析，揭示了影响起始位点效率的染色质背景。

【总体实验设计】：将酵母细胞从α因子阻滞中释放，于T=0分钟（释放前）开始，每10分钟收集一次样本，采集时长覆盖释放后0至150分钟（重复1）或0至140分钟（重复2）。由于重复1的α因子阻滞恢复时长较重复2多出一个时间点，因此在对齐两个重复的细胞周期时间线时，丢弃重复1的T=10分钟样本，并将后续所有时间点整体前移一个时间点。本研究设置两个生物学重复，共包含30例MNase染色质测序样本与29例RNA测序样本（重复2的T=110分钟样本质量不佳，予以丢弃）。