Intronic Polyadenylation Derived Long Non-coding RNA modulates Nucleolar Integrity and Function

Intronic polyadenylation (IPA) events occurring near the transcription start site or within early introns can generate numerous non-coding RNAs derived from protein-coding loci (ncpRNAs). Despite their abundance, the functional roles of ncpRNAs remain largely unexplored. In this study, we characterized one such long non-coding RNA, ncpCUL1, transcribed from the CUL1 gene locus. Our results revealed that ncpCUL1 is a polyadenylated, RNA polymerase II dependent IPA isoform that is stable and translocates to the nucleolus. Functional characterization demonstrated that ncpCUL1 plays a critical role in maintaining nucleolar integrity. RNA-protein interaction assays identified GPATCH4 and NOP58, two nucleolar proteins involved in rRNA processing, as binding partners of ncpCUL1. Consistent with its localization and interactions, loss of ncpCUL1 led to a reduction in rRNA levels and consequent decrease in protein synthesis. This effect on rRNA levels could be reversed by reintroducing ncpCUL1, confirming its functional importance. Furthermore, as nucleolar stress is known to affect cell cycle progression, we found that ncpCUL1 depletion resulted in G2 phase cell cycle arrest. Together, our findings demonstrate that ncpCUL1, an IPA-derived lncRNA from the CUL1 locus, forms an RNA-protein complex in the nucleolus to support nucleolar structure and function.