RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites

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

doi:10.1016/j.cell.2014.08.018

RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites

Cell. 2014 Sep 25;159(1):188-199. doi: 10.1016/j.cell.2014.08.018.

Authors

Affiliations

¹ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA.
² Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
³ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
⁴ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA.
⁵ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address: mguttman@caltech.edu.
⁶ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA. Electronic address: lander@broadinstitute.org.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Base Sequence
Cross-Linking Reagents / metabolism
Genetic Techniques*
Mice
Molecular Sequence Data
Nucleotide Motifs
RNA Splice Sites
RNA, Long Noncoding / chemistry
RNA, Long Noncoding / metabolism
RNA, Messenger / chemistry
RNA, Messenger / metabolism*
RNA, Small Nuclear / metabolism
RNA, Untranslated / chemistry
RNA, Untranslated / metabolism

Substances

Cross-Linking Reagents
Malat1 long non-coding RNA, mouse
RNA Splice Sites
RNA, Long Noncoding
RNA, Messenger
RNA, Small Nuclear
RNA, Untranslated
U1 small nuclear RNA

Associated data

GEO/GSE55914

Abstract

Publication types

MeSH terms

Substances

Associated data

Grants and funding