title: Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis.
abstract: The SMARCA4 (also known as BRG1 in humans) chromatin remodeling factor is critical for establishing lineage-specific chromatin states during early mammalian development. However, the role of SMARCA4 in tissue-specific gene regulation during embryogenesis remains poorly defined. To investigate the genome-wide binding landscape of SMARCA4 in differentiating tissues, we engineered a Smarca4(FLAG) knock-in mouse line. Using ChIP-seq, we identified ∼51,000 SMARCA4-associated regions across six embryonic mouse tissues (forebrain, hindbrain, neural tube, heart, limb, and face) at mid-gestation (E11.5). The majority of these regions was distal from promoters and showed dynamic occupancy, with most distal SMARCA4 sites (73%) confined to a single or limited subset of tissues. To further characterize these regions, we profiled active and repressive histone marks in the same tissues and examined the intersection of informative chromatin states and SMARCA4 binding. This revealed distinct classes of distal SMARCA4-associated elements characterized by activating and repressive chromatin signatures that were associated with tissue-specific up- or down-regulation of gene expression and relevant active/repressed biological pathways. We further demonstrate the predicted active regulatory properties of SMARCA4-associated elements by retrospective analysis of tissue-specific enhancers and direct testing of SMARCA4-bound regions in transgenic mouse assays. Our results indicate a dual active/repressive function of SMARCA4 at distal regulatory sequences in vivo and support its role in tissue-specific gene regulation during embryonic development.
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Catia
authors.initials: C
authors.lastname: Attanasio
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Alex S
authors.initials: AS
authors.lastname: Nord
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Yiwen
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA;
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Blow
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; Addenbrooke's Hospital, Cambridge University NHS Trust, Cambridge CB2 0QQ, United Kingdom;
authors.forename: Simon C
authors.initials: SC
authors.lastname: Biddie
authors.affiliation: HHMI and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA;
authors.forename: Eric M
authors.initials: EM
authors.lastname: Mendenhall
authors.affiliation: Ludwig Institute for Cancer Research, UCSD School of Medicine, La Jolla, California 92093, USA.
authors.forename: Jesse
authors.initials: J
authors.lastname: Dixon
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA;
authors.forename: Crystal
authors.initials: C
authors.lastname: Wright
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Roya
authors.initials: R
authors.lastname: Hosseini
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Akiyama
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Amy
authors.initials: A
authors.lastname: Holt
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Ingrid
authors.initials: I
authors.lastname: Plajzer-Frick
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Malak
authors.initials: M
authors.lastname: Shoukry
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Veena
authors.initials: V
authors.lastname: Afzal
authors.affiliation: Ludwig Institute for Cancer Research, UCSD School of Medicine, La Jolla, California 92093, USA.
authors.forename: Bing
authors.initials: B
authors.lastname: Ren
authors.affiliation: HHMI and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA;
authors.forename: Bradley E
authors.initials: BE
authors.lastname: Bernstein
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA;
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA;
authors.forename: Axel
authors.initials: A
authors.lastname: Visel
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA;
authors.forename: Len A
authors.initials: LA
authors.lastname: Pennacchio
mesh_terms: D000818:Animals; D001921:Brain / Q000196:embryology / Q000378:metabolism; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D004265:DNA Helicases / Q000235:genetics / Q000378:metabolism*; D005121:Extremities / Q000196:embryology; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D006321:Heart / Q000196:embryology; D006657:Histones / Q000235:genetics / Q000378:metabolism; D051379:Mice; D009206:Myocardium / Q000378:metabolism; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D009928:Organ Specificity; D011485:Protein Binding; D050436:Regulatory Elements, Transcriptional; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D002843:Chromatin; D006657:Histones; D009687:Nuclear Proteins; D014157:Transcription Factors; C513194:Smarca4 protein, mouse; D004265:DNA Helicases
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