Multiple modes of regulation control dynamic transcription patterns during the mitosis-G1 transition

Following cell division, genomes must reactivate gene expression patterns that reflect the identity of the cell. Here, we use PRO-seq to examine the mechanisms that reestablish transcription patterns after mitosis. We uncover regulation of the transcription cycle at multiple steps including initiation, promoter-proximal pause positioning and escape, poly-A site cleavage and termination during the mitotic-G1 transition. During mitosis, RNA polymerase activity is retained at initiation sites, albeit shifted in position relative to non-mitotic cells. This activity is strongly linked to maintenance of local chromatin architecture during mitosis and is more predictive of rapid gene reactivation than histone modifications previously associated with bookmarking. These molecular bookmarks, combined with sequence-specific transcription factors, direct expression of select cell growth and cell specific genes during mitosis followed by reactivation of functional gene groups with distinct kinetics after mitosis. This study details how dynamic regulation of transcription at multiple steps contributes to gene expression during the cell cycle. Profiling of nascent transcription (PRO-seq) and chromatin accessibility (ATAC-seq) during and after release from mitosis in HeLa-S3 and HEK293T cells.

细胞分裂完成后，基因组需重新激活契合细胞身份的基因表达模式。本研究采用精准核连转录测序（PRO-seq）技术，探究有丝分裂后转录模式重建的分子机制。我们揭示了有丝分裂-G1期转换过程中转录周期的多步骤调控机制，涵盖转录起始、启动子近端暂停的定位与逃逸、多聚腺苷酸化位点切割及转录终止等环节。有丝分裂期间，RNA聚合酶（RNA polymerase）活性仍保留于转录起始位点，不过其结合位置相较于非有丝分裂细胞发生了偏移。该活性与有丝分裂期间局部染色质结构的维持紧密相关，且相较于此前被归为转录书签（bookmarking）的组蛋白修饰，其对基因快速重激活的预测能力更强。这些分子书签与序列特异性转录因子协同，在有丝分裂期间调控特定细胞生长基因与细胞类型特异性基因的表达，并在有丝分裂结束后，驱动不同动力学特征的功能基因群相继重激活。本研究阐明了转录多步骤的动态调控如何助力细胞周期进程中的基因表达调控。本研究对HeLa-S3与HEK293T细胞在有丝分裂期间及脱离有丝分裂后的新生转录组（PRO-seq）与染色质可及性（ATAC-seq）进行了测序分析。