RNA subcellular localization often correlates with its function and regulation. For many long noncoding RNAs (lncRNAs) and some isoforms of coding genes, their transcripts are preferentially retained in the nucleus. However, the mechanisms controlling the nuclear retention of lncRNAs and mRNA transcripts remain largely unknown. We hypothesize that embedded RNA sequences and interacting proteins may be the cis and trans regulators governing RNA subcellular localization, respectively. To comprehensively identify the cis-regulatory elements of RNA transcript, here we have developed a high-throughput sequencing-based method named RNA subcellular localization profiling (RSLP). Using this method, we identified RNA sequences contribute to the nuclear retention of several transcripts. By combining RSLP with random mutagenesis (mutRSLP), we further narrowed down the key RNA motifs and residues in regulating their subcellular localization at base resolution. Finally, based on the RNA element we identified, we revealed and confirmed U1 snRNA targeting site contributes to RNA nuclear retention. SOURCE: Yuyang Lu (bioyuyang@hotmail.com) -  Tsinghua University

Pluto Bioinformatics

GSE107131: U1 snRNP regulates chromatin retention of noncoding RNAs