Antagonism between splicing and microprocessor complex dictates the serum-induced processing of lnc-<i>MIRHG</i> for efficient cell cycle reentry

Abstract

Cellular quiescence and cell cycle reentry regulate vital biological processes such as cellular development and tissue homeostasis and are controlled by precise regulation of gene expression. The roles of long noncoding RNAs (lncRNAs) during these processes remain to be elucidated. By performing genome-wide transcriptome analyses, we identify differential expression of several hundreds of lncRNAs, including a significant number of the less-characterized class of microRNA-host-gene (<i>MIRHG</i>) lncRNAs or lnc-<i>MIRHGs</i>, during cellular quiescence and cell cycle reentry in human diploid fibroblasts. We observe that <i>MIR222HG</i> lncRNA displays serum-stimulated RNA processing due to enhanced splicing of the host nascent pri-<i>MIR222HG</i> transcript. The pre-mRNA splicing factor SRSF1 negatively regulates the microprocessor-catalyzed cleavage of pri-miR-222, thereby increasing the cellular pool of the mature <i>MIR222HG</i> Association of SRSF1 to pri-<i>MIR222HG</i>, including to a mini-exon, which partially overlaps with the primary miR-222 precursor, promotes serum-stimulated splicing over microRNA processing of <i>MIR222HG</i> Further, we observe that the increased levels of spliced <i>MIR222HG</i> in serum-stimulated cells promote the cell cycle reentry post quiescence in a microRNA-independent manner. <i>MIR222HG</i> interacts with <i>DNM3OS</i>, another lncRNA whose expression is elevated upon serum-stimulation, and promotes cell cycle reentry. The double-stranded RNA binding protein ILF3/2 complex facilitates <i>MIR222HG</i>:<i>DNM3OS</i> RNP complex assembly, thereby promoting <i>DNM3OS</i> RNA stability. Our study identifies a novel mechanism whereby competition between the splicing and microprocessor machinery modulates the serum-induced RNA processing of <i>MIR222HG</i>, which dictates cell cycle reentry.