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High-throughput identification of RNA nuclear enrichment sequences

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Item Type:Article
Title:High-throughput identification of RNA nuclear enrichment sequences
Creators Name:Shukla, C.J. and McCorkindale, A.L. and Gerhardinger, C. and Korthauer, K.D. and Cabili, M.N. and Shechner, D.M. and Irizarry, R.A. and Maass, P. and Rinn, J.L.
Abstract:In the post-genomic era, thousands of putative noncoding regulatory regions have been identified, such as enhancers, promoters, long noncoding RNAs (lncRNAs), and a cadre of small peptides. These ever-growing catalogs require high-throughput assays to test their functionality at scale. Massively parallel reporter assays have greatly enhanced the understanding of noncoding DNA elements en masse Here, we present a massively parallel RNA assay (MPRNA) that can assay 10,000 or more RNA segments for RNA-based functionality. We applied MPRNA to identify RNA-based nuclear localization domains harbored in lncRNAs. We examined a pool of 11,969 oligos densely tiling 38 human lncRNAs that were fused to a cytosolic transcript. After cell fractionation and barcode sequencing, we identified 109 unique RNA regions that significantly enriched this cytosolic transcript in the nucleus including a cytosine-rich motif. These nuclear enrichment sequences are highly conserved and over-represented in global nuclear fractionation sequencing. Importantly, many of these regions were independently validated by single-molecule RNA fluorescence in situ hybridization. Overall, we demonstrate the utility of MPRNA for future investigation of RNA-based functionalities.
Keywords:De Novo Inference Of Regions, High-Throughput Reporter Assay, lncRNA, Nuclear Localization, RNA
Source:EMBO Journal
ISSN:0261-4189
Publisher:EMBO Press
Volume:37
Page Range:e98452
Date:15 March 2018
Official Publication:https://doi.org/10.15252/embj.201798452
PubMed:View item in PubMed

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