10779/crick.12681905.v1 Tiago Faial Tiago Faial Andreia S Bernardo Andreia S Bernardo Sasha Mendjan Sasha Mendjan Evangelia Diamanti Evangelia Diamanti Daniel Ortmann Daniel Ortmann George E Gentsch George E Gentsch Victoria L Mascetti Victoria L Mascetti Matthew WB Trotter Matthew WB Trotter James C Smith James C Smith Roger A Pedersen Roger A Pedersen Brachyury and SMAD signalling collaboratively orchestrate distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells The Francis Crick Institute 2020 Embryonic stem cells Gastrulation Gene regulatory networks Human SMAD T-BOX Animals Bone Morphogenetic Protein 4 Cell Line Embryonic Stem Cells Endoderm Fetal Proteins Gene Expression Regulation, Developmental Humans Mesoderm Mice Mice, Transgenic Neurogenesis Smad1 Protein Smad2 Protein Smad3 Protein T-Box Domain Proteins Smith U117597140 AS-ack 06 Biological Sciences 11 Medical and Health Sciences 2020-07-21 11:31:05 Journal contribution https://crick.figshare.com/articles/journal_contribution/Brachyury_and_SMAD_signalling_collaboratively_orchestrate_distinct_mesoderm_and_endoderm_gene_regulatory_networks_in_differentiating_human_embryonic_stem_cells/12681905 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.