Joint cell cycle profiling of RNA, RNA polymerase, and active promoters identify non-coding RNAs involved in cell cycle progression and proliferation

Proper regulation of the cell cycle is necessary for normal growth and development of all organisms. Understanding this regulation is important in the study of proliferative diseases such as cancer. Long non-coding RNAs (lncRNAs) are recognized as important regulators of gene expression and are often found dysregulated in several diseases. Due to the regulatory role of several lncRNAs, they are likely to be involved in cancer progression. Also, with their high cell type specificity, lncRNAs might represent novel therapeutic targets and biomarkers for diagnostics. Here, we propose a highly effective method for the identification of genes enriched for cell cycle functions. By combining RNA sequencing with ChIP sequencing of synchronized HaCaT cells we identified 1803 cell cycle-associated genes, of which 99 were lncRNAs. Based on the RNA sequencing results and their correlation with RNA polymerase II, H3K4me3, and H3K27me3 ChIP sequencing signal, four of these lncRNAs were selected for further experimental validation. We show that siRNA-mediated knockdown of these lncRNAs affected cell cycle phase distributions and reduced cell growth in multiple cell lines.