Profiling and characterization of constitutive chromatin-enriched RNAs

Wenlong Shen; Yan Zhang; Minglei Shi; Bingyu Ye; Man Yin; Ping Li; Shu Shi; Yifei Jin; Zhang Zhang; Michael Q Zhang; Yang Chen; Zhihu Zhao

doi:10.1016/j.isci.2022.105349

Profiling and characterization of constitutive chromatin-enriched RNAs

iScience. 2022 Oct 13;25(11):105349. doi: 10.1016/j.isci.2022.105349. eCollection 2022 Nov 18.

Authors

Wenlong Shen¹, Yan Zhang¹, Minglei Shi², Bingyu Ye³, Man Yin⁴, Ping Li¹, Shu Shi¹, Yifei Jin¹, Zhang Zhang¹, Michael Q Zhang², Yang Chen⁵, Zhihu Zhao¹

Affiliations

¹ Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China.
² MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, BNRIST/School of Medicine, Tsinghua University, Beijing 100084, China.
³ College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
⁴ Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
⁵ The State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.

Abstract

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.

Keywords: Biological sciences; Molecular biology; Systems biology.