RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites
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Author(s)
Sirokman, Klara
McDonel, Patrick
Shishkin, Alexander A.
Surka, Christine
Russell, Pamela
Chow, Amy Y.
Guttman, Mitchell
Lander, Eric Steven
Engreitz, Jesse Michael
Grossman, Sharon Rachel
Date Issued
September 2014
Journal
Cell
Publisher
Elsevier
Citation
Engreitz, Jesse M. et al. “RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites.” Cell 159.1 (2014): 188–199.
Version
Author's final manuscript
Abstract
Intermolecular RNA-RNA interactions are used by many noncoding RNAs (ncRNAs) to achieve their diverse functions. To aid in identifying 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 snRNA, a component of the spliceosome, and Malat1, a lncRNA 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 both 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 premRNAs and genomic sites. RAP-RNA is sensitive to lower abundance RNAs as well, making it generally applicable for investigating ncRNAs.
MIT Department
Harvard University--MIT Division of Health Sciences and Technology
Massachusetts Institute of Technology. Department of Biology
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DOI of Published Version
https://doi.org/10.1016/j.cell.2014.08.018
