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High-throughput identification of RNA nuclear enrichment sequences

Chinmay J Shukla, Alexandra L McCorkindale, Chiara Gerhardinger, Keegan D Korthauer, Moran N Cabili, David M Shechner, Rafael A Irizarry, Philipp G Maass, John L Rinn
doi: https://doi.org/10.1101/189654
Chinmay J Shukla
1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Cambridge, Massachusetts 02115, USA
4Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts 02115, USA
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Alexandra L McCorkindale
1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
7Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin-Buch 13125, Germany
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Chiara Gerhardinger
1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
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Keegan D Korthauer
3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Cambridge, Massachusetts 02115, USA
5Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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Moran N Cabili
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
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David M Shechner
1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
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Rafael A Irizarry
3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Cambridge, Massachusetts 02115, USA
5Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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Philipp G Maass
1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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John L Rinn
1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
6Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
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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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted September 15, 2017.
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High-throughput identification of RNA nuclear enrichment sequences
Chinmay J Shukla, Alexandra L McCorkindale, Chiara Gerhardinger, Keegan D Korthauer, Moran N Cabili, David M Shechner, Rafael A Irizarry, Philipp G Maass, John L Rinn
bioRxiv 189654; doi: https://doi.org/10.1101/189654
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High-throughput identification of RNA nuclear enrichment sequences
Chinmay J Shukla, Alexandra L McCorkindale, Chiara Gerhardinger, Keegan D Korthauer, Moran N Cabili, David M Shechner, Rafael A Irizarry, Philipp G Maass, John L Rinn
bioRxiv 189654; doi: https://doi.org/10.1101/189654

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