GSE134287
U1 snRNP regulates chromatin retention of noncoding RNAs
Pervasive transcription in the mammalian genome produces thousands of long noncoding RNAs (lncRNAs) and promoter- or enhancer-associated unstable transcripts. They preferentially locate to chromatin, at which some regulate chromatin structure, transcription and RNA processing. While several RNA sequences responsible for nuclear localization have been identified, such as repeats in the lncRNA Xist and Alu-like elements for long RNAs, how lncRNAs as a class are enriched on chromatin remains elusive. To screen for cis-elements that contribute to RNA-chromatin localization, we developed a high-throughput method named RNA elements for subcellular localization by sequencing (REL-seq), and discovered a U1 small nuclear ribonucleoprotein (snRNP)-recognition motif being critical for chromatin localization of reporter RNAs. Across the genome, chromatin-bound lncRNAs, which are enriched with 5' splice sites and depleted of 3' splice sites, exhibit high levels of U1 snRNA binding compared to cytoplasm-localized protein-coding mRNAs. Acute depletion of U1 snRNA, or U1 snRNP protein component SNRNP70, drastically reduces the chromatin association of hundreds of lncRNAs and unstable transcripts without altering the overall transcription rate in cells. In addition, rapid degradation of SNRNP70 reduces the localization of both nascent and polyadenylated lncRNA transcripts to chromatin, and disrupts the nuclear-speckles and genome-wide localization of Malat1, a highly conserved and abundant lncRNA. Moreover, chromatin-bound U1 snRNP interacts with transcriptionally engaged RNA polymerase (Pol) II. Together, these results demonstrate that U1 snRNP acts widely to tether and mobilize lncRNAs to chromatin in a Pol II transcription-dependent manner. Our findings uncover a novel role of U1 snRNP beyond pre-mRNA processing and provide molecular insights into how lncRNAs are recruited to Pol II-transcribed genes and have a propensity for chromatin-associated functions. Overall design: All RNA-seq were used to identify the subcellular localization changes of lncRNAs upon U1 AMO inhibtion or SNRNP70AID degradation. Total RNA-seq identifies both nascent and mature RNAs; polyA RNA-seq mainly identifies mature RNAs; SLAM-seq was used to discriminate newly-synthesized polyA RNA after SNRNP70AID degradation from pre-existed RNAs. All ChIP-seq and TT-seq were used to chracterize the changes of Ser5 or Ser2 phosphorylated Pol II occupancy and transcription rate upon SNRNP70 acute degradation. All ChIRP-seq were used to characterize the changes of Malat1 genome-wide targeting upon SNRNP70 acute depletion or transcription inhibition.