Shen Wenlong, Zhang Yan, Shi Minglei, Ye Bingyu, Yin Man, Li Ping, Shi Shu, Jin Yifei, Zhang Zhang, Zhang Michael Q, Chen Yang, Zhao Zhihu
Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China.
MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, BNRIST/School of Medicine, Tsinghua University, Beijing 100084, China.
iScience. 2022 Oct 13;25(11):105349. doi: 10.1016/j.isci.2022.105349. eCollection 2022 Nov 18.
RNA species act as architectural scaffolds for nuclear structures including chromatin in eukaryotic cells. However, the composition and dynamics of tightly bound chromatin-associated RNAs during mitosis remains elusive. Here we report the identification of chromatin-enriched RNA (cheRNAs) by biochemical nuclear fractionation coupled with RNA sequencing in both interphase and mitotic phase of A549 and HeLa-S3 cell lines. We show that highly abundant cheRNAs, mostly small noncoding RNAs, are largely maintained in mitotic chromatin, and constitute a substantial part of chromatin RNA throughout cell cycle. We also show that the mitotic retained cheRNAs tend to be cell type nonspecific and might be involved in chromatin accessibility and epigenetic memory of gene expression control. Therefore, we reveal an unexpected set of cell type-nonspecific mitotic retained chromatin-enriched RNAs. We anticipate that the landscape of RNA composition of chromatin both in interphase and mitotic phase would help understanding structure and function of chromatin.
RNA 种类在真核细胞中作为包括染色质在内的核结构的结构支架。然而，有丝分裂期间紧密结合的染色质相关 RNA 的组成和动态变化仍然不清楚。在这里，我们报告通过生化细胞核分级分离结合 RNA 测序，在 A549 和 HeLa-S3 细胞系的间期和有丝分裂期鉴定出富含染色质的 RNA（cheRNAs）。我们表明，高度丰富的 cheRNAs，主要是小非编码 RNA，在有丝分裂染色质中基本得以保留，并且在整个细胞周期中构成染色质 RNA 的很大一部分。我们还表明，有丝分裂保留的 cheRNAs 倾向于细胞类型非特异性，并且可能参与染色质可及性和基因表达控制的表观遗传记忆。因此，我们揭示了一组意想不到的细胞类型非特异性有丝分裂保留的富含染色质的 RNA。我们预计，间期和有丝分裂期染色质的 RNA 组成情况将有助于理解染色质的结构和功能。
