Profiling and characterization of constitutive chromatin-enriched RNAs

• Published in: iScience Vol. 25; no. 11; p. 105349
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 18.11.2022; Elsevier
• Subjects: Biological sciences; Molecular biology; Systems biology; Molecular biology; Systems biology; Biological sciences
• ISSN: 2589-0042; 2589-0042
• DOI: 10.1016/j.isci.2022.105349

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. [Display omitted] •Chromatin-enriched RNAs are largely maintained in mitotic cells•Mitotic retained cheRNAs are stable abundant, enriched in small noncoding RNAs•Mitotic retained cheRNAs tend to be cell type nonspecific•DNA targets of mitotic retained cheRNAs in interphase remain active in mitotic phase Biological sciences; Molecular biology; Systems biology