High-throughput identification of RNA nuclear enrichment sequences
High-throughput identification of RNA nuclear enrichment sequences
Summary One of the biggest surprises since the sequencing of the human genome has been the discovery of thousands of long noncoding RNAs (lncRNAs)1–6. Although lncRNAs and mRNAs are similar in many ways, they differ with lncRNAs being more nuclear-enriched and in several cases exclusively nuclear7,8. Yet, the RNA-based sequences that determine nuclear localization remain poorly understood9–11. Towards the goal of systematically dissecting the lncRNA sequences that impart nuclear localization, we developed a massively parallel reporter assay (MPRA). Unlike previous MPRAs12–15 that determine motifs important for transcriptional regulation, we have modified this approach to identify sequences sufficient for RNA nuclear enrichment for 38 human lncRNAs. Using this approach, we identified 109 unique, conserved nuclear enrichment regions, originating from 29 distinct lncRNAs. We also discovered two shorter motifs within our nuclear enrichment regions. We further validated the sufficiency of several regions to impart nuclear localization by single molecule RNA fluorescence in situ hybridization (smRNA-FISH). Taken together, these results provide a first systematic insight into the sequence elements responsible for the nuclear enrichment of lncRNA molecules.
Shukla Chinmay J、McCorkindale Alexandra L、Shechner David M、Maass Philipp G、Cabili Moran N、Gerhardinger Chiara、Korthauer Keegan D、Rinn John L、Irizarry Rafael A
Department of Stem Cell and Regenerative Biology, Harvard University||Broad Institute of MIT and Harvard||Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute||Program in Biological and Biomedical Sciences, Harvard Medical SchoolDepartment of Stem Cell and Regenerative Biology, Harvard University||Berlin Institute for Medical Systems Biology, Max Delbr¨1ck Center for Molecular MedicineDepartment of Stem Cell and Regenerative Biology, Harvard University||Broad Institute of MIT and HarvardDepartment of Stem Cell and Regenerative Biology, Harvard UniversityBroad Institute of MIT and HarvardDepartment of Stem Cell and Regenerative Biology, Harvard University||Broad Institute of MIT and HarvardDepartment of Biostatistics and Computational Biology, Dana-Farber Cancer Institute||Department of Biostatistics, Harvard T.H. Chan School of Public HealthDepartment of Stem Cell and Regenerative Biology, Harvard University||Broad Institute of MIT and Harvard||Department of Pathology, Beth Israel Deaconess Medical CenterDepartment of Biostatistics and Computational Biology, Dana-Farber Cancer Institute||Department of Biostatistics, Harvard T.H. Chan School of Public Health
分子生物学遗传学生物科学研究方法、生物科学研究技术
Shukla Chinmay J,McCorkindale Alexandra L,Shechner David M,Maass Philipp G,Cabili Moran N,Gerhardinger Chiara,Korthauer Keegan D,Rinn John L,Irizarry Rafael A.High-throughput identification of RNA nuclear enrichment sequences[EB/OL].(2025-03-28)[2025-05-31].https://www.biorxiv.org/content/10.1101/189654.点此复制
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