title: Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling.
abstract: Transcription-regulating long non-coding RNAs (lncRNAs) have the potential to control the site-specific expression of thousands of target genes. Previously, we showed that Evf2, the first described ultraconserved lncRNA, increases the association of transcriptional activators (DLX homeodomain proteins) with key DNA enhancers but represses gene expression. In this report, mass spectrometry shows that the Evf2-DLX1 ribonucleoprotein (RNP) contains the SWI/SNF-related chromatin remodelers Brahma-related gene 1 (BRG1, SMARCA4) and Brahma-associated factor (BAF170, SMARCC2) in the developing mouse forebrain. Evf2 RNA colocalizes with BRG1 in nuclear clouds and increases BRG1 association with key DNA regulatory enhancers in the developing forebrain. While BRG1 directly interacts with DLX1 and Evf2 through distinct binding sites, Evf2 directly inhibits BRG1 ATPase and chromatin remodeling activities. In vitro studies show that both RNA-BRG1 binding and RNA inhibition of BRG1 ATPase/remodeling activity are promiscuous, suggesting that context is a crucial factor in RNA-dependent chromatin remodeling inhibition. Together, these experiments support a model in which RNAs convert an active enhancer to a repressed enhancer by directly inhibiting chromatin remodeling activity, and address the apparent paradox of RNA-mediated stabilization of transcriptional activators at enhancers with a repressive outcome. The importance of BRG1/RNA and BRG1/homeodomain interactions in neurodevelopmental disorders is underscored by the finding that mutations in Coffin-Siris syndrome, a human intellectual disability disorder, localize to the BRG1 RNA-binding and DLX1-binding domains.
authors.affiliation: Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA.
authors.forename: Ivelisse
authors.initials: I
authors.lastname: Cajigas
authors.affiliation: Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Leib
authors.affiliation: Department of Molecular Biology, Harvard University, Boston, MA 02114, USA.
authors.forename: Jesse
authors.initials: J
authors.lastname: Cochrane
authors.affiliation: Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Luo
authors.affiliation: Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA.
authors.forename: Kelsey R
authors.initials: KR
authors.lastname: Swyter
authors.affiliation: Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA.
authors.forename: Sean
authors.initials: S
authors.lastname: Chen
authors.affiliation: Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA.
authors.forename: Brian S
authors.initials: BS
authors.lastname: Clark
authors.affiliation: The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: James
authors.initials: J
authors.lastname: Thompson
authors.affiliation: The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
authors.affiliation: Department of Molecular Biology, Harvard University, Boston, MA 02114, USA.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Kingston
authors.affiliation: Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA j-kohtz@northwestern.edu.
authors.forename: Jhumku D
authors.initials: JD
authors.lastname: Kohtz
mesh_terms: D000015:Abnormalities, Multiple / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D042002:Chromatin Assembly and Disassembly / Q000235:genetics / Q000502:physiology*; D047369:Chromatin Immunoprecipitation; D004265:DNA Helicases / Q000235:genetics / Q000378:metabolism*; D017931:DNA Primers / Q000235:genetics; D005145:Face / Q000002:abnormalities; D005786:Gene Expression Regulation / Q000235:genetics*; D006228:Hand Deformities, Congenital / Q000235:genetics; D018398:Homeodomain Proteins / Q000378:metabolism*; D006801:Humans; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence; D008607:Intellectual Disability / Q000235:genetics; D013058:Mass Spectrometry; D051379:Mice; D008844:Micrognathism / Q000235:genetics; D008969:Molecular Sequence Data; D009333:Neck / Q000002:abnormalities; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D016548:Prosencephalon / Q000196:embryology*; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism*; D012261:Ribonucleoproteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D017931:DNA Primers; C088334:Distal-less homeobox proteins; D018398:Homeodomain Proteins; D009687:Nuclear Proteins; D062085:RNA, Long Noncoding; D012261:Ribonucleoproteins; D014157:Transcription Factors; C513194:Smarca4 protein, mouse; D004265:DNA Helicases
keywords: BRG1; Chromatin remodeling; Dlx6os1; Evf2; Homeodomain proteins; Long non-coding RNA; SMARCA4