Nuclear fractionation to identify chromatin associated RNA in interphase and M-phase cells [RNA-seq]

The composition and dynamics of tightly bound chromatin associated RNAs during mitosis remains elusive. Here we report identification of chromatin enriched (cheRNAs) by biochemical nuclear fractionation coupled with RNA-seq in both interphase and mitotic phase of A549 and HeLaS3 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 throughout cell cycle. We also show that the mitotic retained cheRNAs tend to be cell type nonspecific. We speculate that these cell type nonspecific cheRNAs might play roles in chromatin state and gene expression control. We anticipate the panoramic landscape of RNA composition of chromatin both in interphase and M-phase would shed light on understanding the structure and function of chromatin in M phase and would also help the understanding of some fundamental biological functions. In this case, for each of A549 cells as well as HeLa-S3 cells, we performed RNA-seq on samples from two independent biological replicates of soluble nuclear extract (S) and chromatin pellet extract (P) both in asynchronized (with interphase accounting for ~95% of cells, we called these cells as “inter-phase cells” afterwards) and M-phase