title: The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites.
abstract: Mechanistic roles for many lncRNAs are poorly understood, in part because their direct interactions with genomic loci and proteins are difficult to assess. Using a method to purify endogenous RNAs and their associated factors, we mapped the genomic binding sites for two highly expressed human lncRNAs, NEAT1 and MALAT1. We show that NEAT1 and MALAT1 localize to hundreds of genomic sites in human cells, primarily over active genes. NEAT1 and MALAT1 exhibit colocalization to many of these loci, but display distinct gene body binding patterns at these sites, suggesting independent but complementary functions for these RNAs. We also identified numerous proteins enriched by both lncRNAs, supporting complementary binding and function, in addition to unique associated proteins. Transcriptional inhibition or stimulation alters localization of NEAT1 on active chromatin sites, implying that underlying DNA sequence does not target NEAT1 to chromatin, and that localization responds to cues involved in the transcription process.
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Jason A
authors.initials: JA
authors.lastname: West
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Christopher P
authors.initials: CP
authors.lastname: Davis
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Hongjae
authors.initials: H
authors.lastname: Sunwoo
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Simon
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Ruslan I
authors.initials: RI
authors.lastname: Sadreyev
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Peggy I
authors.initials: PI
authors.lastname: Wang
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Tolstorukov
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: kingston@molbio.mgh.harvard.edu.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Kingston
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000378:metabolism*; D006801:Humans; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization; D062085:RNA, Long Noncoding / Q000032:analysis / Q000737:chemistry / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; C557041:MALAT1 long non-coding RNA, human; C577276:NEAT1 long non-coding RNA, human; D062085:RNA, Long Noncoding