DNA-guided transcription factor cooperativity shapes face and limb mesenchyme.

ALX factors Coordinator TWIST1 bHLH cooperativity face homeodomain limb mesenchyme neural crest transcription factor

Journal

Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066

Informations de publication

Date de publication:
17 Jan 2024
Historique:
received: 20 04 2023
revised: 23 10 2023
accepted: 27 12 2023
medline: 24 1 2024
pubmed: 24 1 2024
entrez: 23 1 2024
Statut: aheadofprint

Résumé

Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest that it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how "Coordinator," a long DNA motif composed of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines the regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, whereas HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in the shared regulation of genes involved in cell-type and positional identities and ultimately shapes facial morphology and evolution.

Identifiants

DOI: 10.1016/j.cell.2023.12.032 PMID: 38262408
pubmed: 38262408
pii: S0092-8674(23)01438-1
doi: 10.1016/j.cell.2023.12.032
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests J.W. is a paid scientific advisory board member at Camp4 and Paratus Sciences. J.T. has a consultancy agreement with DeepMind Technologies. J.W. is an advisory board member at Cell Press journals, including Cell, Molecular Cell, and Developmental Cell.

Auteurs

Seungsoo Kim (S)

Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.

Ekaterina Morgunova (E)

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.

Sahin Naqvi (S)

Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.

Seppe Goovaerts (S)

Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium.

Maram Bader (M)

Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.

Mervenaz Koska (M)

Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.

Alexander Popov (A)

European Synchrotron Radiation Facility, Grenoble, France.

Christy Luong (C)

Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.

Angela Pogson (A)

Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.

Tomek Swigut (T)

Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.

Peter Claes (P)

Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium; Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.

Jussi Taipale (J)

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden; Department of Biochemistry, University of Cambridge, Cambridge, UK; Applied Tumor Genomics Program, University of Helsinki, Helsinki, Finland.

Joanna Wysocka (J)

Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA. Electronic address: wysocka@stanford.edu.

Classifications MeSH