Specific mitotic chromatin association of the major notch effector RBPJ and its implication for transcriptional memory

From the cell-based investigation, RBPJ is one of the few proteins retained on chromatin during cell division. ChIP-seq experiments were performed to understand the binding pattern of RBPJ between interphase and mitosis and to identify the genes requiring RBPJ binding for the maintenance of transcriptional memory. Our results indicate that ~60% of RBPJ occupancy in interphase is retained on mitotic chromatin, and that accounts for 80% of RBPJ in mitosis. The gene ontology analysis reveals that the genes involved in stem cell maintenance, development and differentiation-related pathways correlated with sites of RBPJ occupancy. GO analysis also suggests that RBPJ plays a role in the metabolism and processing of non-coding RNAs. Motif analysis of RBPJ binding sites reveals that not only RBPJ motif but also CTCF motif are enriched around RBPJ binding sites. From these results, we propose that RBPJ can function as a mitotic bookmark, marking genes for efficient transcriptional activation or repression upon exit from mitosis, and may play a role in higher order chromatin structure by collaborating with CTCF.

基于细胞水平的研究显示，RBPJ是少数在细胞分裂过程中仍保留在染色质上的蛋白质之一。为探究RBPJ在间期（interphase）与有丝分裂期（mitosis）的结合模式，并鉴定出维持转录记忆需要RBPJ结合的靶基因，本研究开展了染色质免疫共沉淀测序（ChIP-seq）实验。研究结果表明，间期内约60%的RBPJ结合位点会在有丝分裂染色质上得以保留，且该部分结合位点占有丝分裂期RBPJ总结合位点的80%。基因本体论（Gene Ontology, GO）分析显示，与RBPJ结合位点相关的基因富集于干细胞维持、发育及分化相关通路。GO分析还进一步揭示，RBPJ在非编码RNA的代谢与加工过程中发挥作用。对RBPJ结合位点的基序（Motif）分析表明，RBPJ结合位点周围不仅富集RBPJ基序，同时也富集CTCF基序。基于上述实验结果，我们提出假说：RBPJ可作为有丝分裂书签，标记那些在细胞退出有丝分裂后需要高效激活或沉默的基因；此外，RBPJ还可通过与CTCF协同作用，参与染色质高级结构的构建。