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RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

Engreitz, Jesse M. and Sirokman, Klara and McDonel, Patrick and Shishkin, Alexander A. and Surka, Christine and Russell, Pamela and Grossman, Sharon R. and Chow, Amy Y. and Guttman, Mitchell and Lander, Eric S. (2014) RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites. Cell, 159 (1). pp. 188-199. ISSN 0092-8674. PMCID PMC4177037. https://resolver.caltech.edu/CaltechAUTHORS:20141002-105821728

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Abstract

Intermolecular RNA-RNA interactions are used by many noncoding RNAs (ncRNAs) to achieve their diverse functions. To identify these contacts, we developed a method based on RNA antisense purification to systematically map RNA-RNA interactions (RAP-RNA) and applied it to investigate two ncRNAs implicated in RNA processing: U1 small nuclear RNA, a component of the spliceosome, and Malat1, a large ncRNA that localizes to nuclear speckles. U1 and Malat1 interact with nascent transcripts through distinct targeting mechanisms. Using differential crosslinking, we confirmed that U1 directly hybridizes to 5′ splice sites and 5′ splice site motifs throughout introns and found that Malat1 interacts with pre-mRNAs indirectly through protein intermediates. Interactions with nascent pre-mRNAs cause U1 and Malat1 to localize proximally to chromatin at active genes, demonstrating that ncRNAs can use RNA-RNA interactions to target specific pre-mRNAs and genomic sites. RAP-RNA is sensitive to lower abundance RNAs as well, making it generally applicable for investigating ncRNAs.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://www.cell.com/cell/abstract/S0092-8674%2814%2901050-2PublisherArticle
http://dx.doi.org/10.1016/j.cell.2014.08.018DOIArticle
http://www.sciencedirect.com/science/article/pii/S0092867414010502PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177037/PubMed CentralArticle
ORCID:
AuthorORCID
Engreitz, Jesse M.0000-0002-5754-1719
Guttman, Mitchell0000-0003-4748-9352
Lander, Eric S.0000-0003-2662-4631
Additional Information:© 2014 Elsevier Inc. Received: March 19, 2014. Revised: June 20, 2014. Accepted: August 18, 2014. Published: September 25, 2014. We thank Amy Pandya-Jones for chromatin fractionation protocols; Xuebing Wu for assistance with scoring 50ss motif matches; Tarjei Mikkelsen for assistance with oligonucleotide synthesis; Phil Sharp, Jason West, and Chris Davis for helpful discussions; and Leslie Gaffney for assistance with figures. This work was supported by the Fannie and John Hertz Foundation (J.M.E.), National Defense Science and Engineering Graduate Fellowship (J.M.E.), NIH Director’s Early Independence Award DP5OD012190 (M.G.), Edward Mallincrodt Jr. Foundation (M.G.), Searle Scholars program (M.G.), the Broad Institute of MIT and Harvard (E.S.L. and M.G.), and the California Institute of Technology (M.G.). J.M.E., E.S.L., and M.G. are inventors on a patent application from the Broad Institute that covers the selective purification of RNA bound molecular complexes in cells. Author Contributions: All authors designed experiments and analyses and approved the final manuscript. J.M.E. and K.S. performed experiments. J.M.E. performed computational analyses. J.M.E., P.M., A.Y.C., K.S., A.S., C.S., and M.G. developed experimental protocols. J.M.E., P.R., S.R.G., M.G., and E.S.L. developed analytical methods and tools. J.M.E. and M.G. conceived and designed the study. J.M.E., M.G., and E.S.L. wrote the manuscript.
Funders:
Funding AgencyGrant Number
Fannie and John Hertz FoundationUNSPECIFIED
National Defense Science and Engineering Graduate (NDSEG) FellowshipUNSPECIFIED
NIHDP5OD012190
Edward Mallincrodt Jr. FoundationUNSPECIFIED
Searle Scholars ProgramUNSPECIFIED
Broad Institute of MIT and HarvardUNSPECIFIED
CaltechUNSPECIFIED
Issue or Number:1
PubMed Central ID:PMC4177037
Record Number:CaltechAUTHORS:20141002-105821728
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20141002-105821728
Official Citation:Jesse M. Engreitz, Klara Sirokman, Patrick McDonel, Alexander A. Shishkin, Christine Surka, Pamela Russell, Sharon R. Grossman, Amy Y. Chow, Mitchell Guttman, Eric S. Lander, RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites, Cell, Volume 159, Issue 1, 25 September 2014, Pages 188-199, ISSN 0092-8674, http://dx.doi.org/10.1016/j.cell.2014.08.018. (http://www.sciencedirect.com/science/article/pii/S0092867414010502)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:50169
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:02 Oct 2014 19:52
Last Modified:09 Mar 2020 13:18

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