title: RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites.
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.
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA.
authors.forename: Jesse M
authors.initials: JM
authors.lastname: Engreitz
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: Klara
authors.initials: K
authors.lastname: Sirokman
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: McDonel
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Shishkin
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Christine
authors.initials: C
authors.lastname: Surka
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Pamela
authors.initials: P
authors.lastname: Russell
authors.affiliation: 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.
authors.forename: Sharon R
authors.initials: SR
authors.lastname: Grossman
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Amy Y
authors.initials: AY
authors.lastname: Chow
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address: mguttman@caltech.edu.
authors.forename: Mitchell
authors.initials: M
authors.lastname: Guttman
authors.affiliation: 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.
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
mesh_terms: D000818:Animals; D001483:Base Sequence; D003432:Cross-Linking Reagents / Q000378:metabolism; D005821:Genetic Techniques; D051379:Mice; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D022821:RNA Splice Sites; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D012342:RNA, Small Nuclear / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000378:metabolism
chemical_list: D003432:Cross-Linking Reagents; C557040:Malat1 long non-coding RNA, mouse; D022821:RNA Splice Sites; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D012342:RNA, Small Nuclear; D022661:RNA, Untranslated; C405483:U1 small nuclear RNA