High-throughput Screening of Sequence Elements Associated with RNA Localization

RNA molecules localize to specific subcellular compartments to perform their biological functions correctly. However, the mechanisms underlying RNA transport and subcellular localization remain poorly understood. In this study, we introduced SRLE-seq (Screening RNA Localization Elements by Sequencing) to identify and prioritize functional sequence elements associated with RNA localization. Our approach successfully recovered known elements and identified 2 novel elements linked to nuclear retention by screening randomized MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) fragments. Within our screening library of 6-mer sequences, SRLE-seq identified 110 6-mers exhibiting functions related to nuclear retention and 49 6-mers associated with nuclear export. Notably, we found that the nuclear retention score derived from SRLE-seq improves predictions of RNA subcellular localization, achieving 72% accuracy when incorporated into a deep learning model. Further experiments demonstrated that these localization-associated 6-mers exert their effects through the regulation of RNA-binding proteins. Our study presents a highly efficient method for prioritizing RNA localization elements via sequencing, establishing a valuable resource for further investigation of RNA-binding protein-mediated RNA subcellular localization.