A single-cell and tissue-scale analysis suite resolves Mixl1’s role in heart development
Magdalena E. Strauss,
Mai-Linh Nu Ton,
Samantha Mason,
Jaana Bagri,
Luke T.G. Harland,
Ivan Imaz-Rosshandler,
Nicola K. Wilson,
Jennifer Nichols,
Richard C.V. Tyser,
Berthold Göttgens,
John C. Marioni,
Carolina Guibentif
Affiliations
Magdalena E. Strauss
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK; Department of Mathematics and Statistics, University of Exeter, Exeter EX4 4PY, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Mai-Linh Nu Ton
Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
Samantha Mason
Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
Jaana Bagri
Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
Luke T.G. Harland
Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
Ivan Imaz-Rosshandler
Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
Nicola K. Wilson
Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
Jennifer Nichols
MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
Richard C.V. Tyser
Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
Berthold Göttgens
Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Corresponding author
John C. Marioni
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK; Corresponding author
Carolina Guibentif
Institute Biomedicine, Department of Microbiology and Immunology, Sahlgrenska Center for Cancer Research, University of Gothenburg, 413 90 Gothenburg, Sweden; Corresponding author
Summary: Perturbation studies using gene knockouts have become a key tool for understanding the roles of regulatory genes in development. However, large-scale studies dissecting the molecular role of development master regulators in every cell type throughout the embryo are technically challenging and scarce. Here, we systematically characterize the knockout effects of the key developmental regulators T/Brachyury and Mixl1 in gastrulation and early organogenesis using single-cell profiling of chimeric mouse embryos. For the analysis of these experimental data, we present COSICC, an effective suite of statistical tools to characterize perturbation effects in complex developing cell populations. We gain insights into T’s role in lateral plate mesoderm, limb development, and posterior intermediate mesoderm specification. Furthermore, we generate Mixl1−/− embryonic chimeras and reveal the role of this key transcription factor in discrete mesoderm lineages, in particular concerning developmental dysregulation of the recently identified juxta-cardiac field.
