title: DIGIT Is a Conserved Long Noncoding RNA that Regulates GSC Expression to Control Definitive Endoderm Differentiation of Embryonic Stem Cells.
abstract: Long noncoding RNAs (lncRNAs) exhibit diverse functions, including regulation of development. Here, we combine genome-wide mapping of SMAD3 occupancy with expression analysis to identify lncRNAs induced by activin signaling during endoderm differentiation of human embryonic stem cells (hESCs). We find that DIGIT is divergent to Goosecoid (GSC) and expressed during endoderm differentiation. Deletion of the SMAD3-occupied enhancer proximal to DIGIT inhibits DIGIT and GSC expression and definitive endoderm differentiation. Disruption of the gene encoding DIGIT and depletion of the DIGIT transcript reveal that DIGIT is required for definitive endoderm differentiation. In addition, we identify the mouse ortholog of DIGIT and show that it is expressed during development and promotes definitive endoderm differentiation of mouse ESCs. DIGIT regulates GSC in trans, and activation of endogenous GSC expression is sufficient to rescue definitive endoderm differentiation in DIGIT-deficient hESCs. Our study defines DIGIT as a conserved noncoding developmental regulator of definitive endoderm.
authors.affiliation: Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Kaveh
authors.initials: K
authors.lastname: Daneshvar
authors.affiliation: Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Joshua V
authors.initials: JV
authors.lastname: Pondick
authors.affiliation: Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Byeong-Moo
authors.initials: BM
authors.lastname: Kim
authors.affiliation: Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Chan
authors.initials: C
authors.lastname: Zhou
authors.affiliation: Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Samuel R
authors.initials: SR
authors.lastname: York
authors.affiliation: Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Jillian A
authors.initials: JA
authors.lastname: Macklin
authors.affiliation: Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
authors.forename: Ameed
authors.initials: A
authors.lastname: Abualteen
authors.affiliation: Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; School of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510405, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Tan
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Alla A
authors.initials: AA
authors.lastname: Sigova
authors.affiliation: Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, Amherst, MA 01003, USA.
authors.forename: Chelsea
authors.initials: C
authors.lastname: Marcho
authors.affiliation: Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, Amherst, MA 01003, USA.
authors.forename: Kimberly D
authors.initials: KD
authors.lastname: Tremblay
authors.affiliation: Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, Amherst, MA 01003, USA.
authors.forename: Jesse
authors.initials: J
authors.lastname: Mager
authors.affiliation: Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Choi
authors.affiliation: Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address: acmullen@mgh.harvard.edu.
authors.forename: Alan C
authors.initials: AC
authors.lastname: Mullen
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics*; D004707:Endoderm / Q000254:growth & development / Q000378:metabolism; D054262:Gastrulation / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D051956:Goosecoid Protein / Q000235:genetics*; D000066449:Human Embryonic Stem Cells / Q000378:metabolism; D006801:Humans; D051379:Mice; D062085:RNA, Long Noncoding / Q000235:genetics*; D015398:Signal Transduction; D051900:Smad3 Protein / Q000235:genetics*
chemical_list: C497992:GSC protein, human; C000625044:GSC-DT lncRNA, human; D051956:Goosecoid Protein; D062085:RNA, Long Noncoding; C497790:SMAD3 protein, human; D051900:Smad3 Protein
keywords: DIGIT, SMAD3; GSC; TGF-β; endoderm; lncRNA