title: Brachyury and SMAD signalling collaboratively orchestrate distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells.
abstract: The transcription factor brachyury (T, BRA) is one of the first markers of gastrulation and lineage specification in vertebrates. Despite its wide use and importance in stem cell and developmental biology, its functional genomic targets in human cells are largely unknown. Here, we use differentiating human embryonic stem cells to study the role of BRA in activin A-induced endoderm and BMP4-induced mesoderm progenitors. We show that BRA has distinct genome-wide binding landscapes in these two cell populations, and that BRA interacts and collaborates with SMAD1 or SMAD2/3 signalling to regulate the expression of its target genes in a cell-specific manner. Importantly, by manipulating the levels of BRA in cells exposed to different signalling environments, we demonstrate that BRA is essential for mesoderm but not for endoderm formation. Together, our data illuminate the function of BRA in the context of human embryonic development and show that the regulatory role of BRA is context dependent. Our study reinforces the importance of analysing the functions of a transcription factor in different cellular and signalling environments.
authors.affiliation: The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK tiago.faial@cantab.net.
authors.forename: Tiago
authors.initials: T
authors.lastname: Faial
authors.affiliation: The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK.
authors.forename: Andreia S
authors.initials: AS
authors.lastname: Bernardo
authors.affiliation: The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK.
authors.forename: Sasha
authors.initials: S
authors.lastname: Mendjan
authors.affiliation: Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0XY, UK.
authors.forename: Evangelia
authors.initials: E
authors.lastname: Diamanti
authors.affiliation: The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK.
authors.forename: Daniel
authors.initials: D
authors.lastname: Ortmann
authors.affiliation: The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
authors.forename: George E
authors.initials: GE
authors.lastname: Gentsch
authors.affiliation: The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK.
authors.forename: Victoria L
authors.initials: VL
authors.lastname: Mascetti
authors.affiliation: The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK.
authors.forename: Matthew W B
authors.initials: MW
authors.lastname: Trotter
authors.affiliation: The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
authors.forename: James C
authors.initials: JC
authors.lastname: Smith
authors.affiliation: The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK.
authors.forename: Roger A
authors.initials: RA
authors.lastname: Pedersen
mesh_terms: D000818:Animals; D055415:Bone Morphogenetic Protein 4 / Q000378:metabolism; D002460:Cell Line; D053595:Embryonic Stem Cells / Q000166:cytology* / Q000378:metabolism; D004707:Endoderm / Q000166:cytology; D005326:Fetal Proteins / Q000378:metabolism*; D054262:Gastrulation / Q000502:physiology; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D008648:Mesoderm / Q000166:cytology; D051379:Mice; D008822:Mice, Transgenic; D055495:Neurogenesis / Q000502:physiology*; D051898:Smad1 Protein / Q000378:metabolism*; D051899:Smad2 Protein / Q000378:metabolism; D051900:Smad3 Protein / Q000378:metabolism; D020825:T-Box Domain Proteins / Q000378:metabolism*; D000098908:Brachyury Protein
chemical_list: D055415:Bone Morphogenetic Protein 4; D005326:Fetal Proteins; D051898:Smad1 Protein; D051899:Smad2 Protein; D051900:Smad3 Protein; D020825:T-Box Domain Proteins; D000098908:Brachyury Protein; C525809:BMP4 protein, human; C491199:EOMES protein, human; C497399:SMAD1 protein, human; C497782:SMAD2 protein, human; C497790:SMAD3 protein, human
keywords: Embryonic stem cells; Gastrulation; Gene regulatory networks; Human; SMAD; T-BOX