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Published January 26, 2021 | Supplemental Material + Published
Journal Article Open

Runx1 and Runx3 drive progenitor to T-lineage transcriptome conversion in mouse T cell commitment via dynamic genomic site switching

Abstract

Runt domain-related (Runx) transcription factors are essential for early T cell development in mice from uncommitted to committed stages. Single and double Runx knockouts via Cas9 show that target genes responding to Runx activity are not solely controlled by the dominant factor, Runx1. Instead, Runx1 and Runx3 are coexpressed in single cells; bind to highly overlapping genomic sites; and have redundant, collaborative functions regulating genes pivotal for T cell development. Despite stable combined expression levels across pro-T cell development, Runx1 and Runx3 preferentially activate and repress genes that change expression dynamically during lineage commitment, mostly activating T-lineage genes and repressing multipotent progenitor genes. Furthermore, most Runx target genes are sensitive to Runx perturbation only at one stage and often respond to Runx more for expression transitions than for maintenance. Contributing to this highly stage-dependent gene regulation function, Runx1 and Runx3 extensively shift their binding sites during commitment. Functionally distinct Runx occupancy sites associated with stage-specific activation or repression are also distinguished by different patterns of partner factor cobinding. Finally, Runx occupancies change coordinately at numerous clustered sites around positively or negatively regulated targets during commitment. This multisite binding behavior may contribute to a developmental "ratchet" mechanism making commitment irreversible.

Additional Information

© 2021 National Academy of Sciences. Published under the PNAS license. Edited by Nancy A. Speck, Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, and approved December 14, 2020 (received for review September 22, 2020). We thank Xun Wang (Caltech) and Joseph Lotem (Weizmann Institute) for helpful critiques of the manuscript; E. Janielle Cuala and Suin Jo for preliminary experiments; Diana Perez, Jamie Tijerina, and Patrick Cannon of the Caltech Flow Cytometry and Cell Sorting Facility for cell sorting; Igor Antoshechkin and Vijaya Kumar of the Jacobs Genetics and Genomics Center for sequencing; Henry Amrhein and Diane Trout for sequence curation and computer support; Ingrid Soto for animal care; Maria Quiloan for mouse breeding supervision; Rochelle Diamond for laboratory management and sorting supervision; and the members of the group of E.V.R. for sharing advice, reagents, and preliminary results. This work was supported by Cancer Research Institute Irvington Postdoctoral Fellowship CRI.SHIN (to B.S.), the Japan Society for the Promotion of Science KAKENHI Grant JP19H03692 (to H.H.), The Mochida Memorial Foundation for Medical and Pharmaceutical Research (H.H.), The Naito Foundation (H.H.), The Yasuda Medical Foundation (H.H.), the SENSHIN Medical Research Foundation (H.H.), the Takeda Science Foundation (H.H.), and US Public Health Service Grants R01AI135200 and R01HD076915 (to E.V.R.). V.R.T. was supported by a Students Training in Advanced Research award from the University of California, Davis. Flow cytometry, sequencing, and bioinformatics facility support were from the Beckman Institute at Caltech. Support was also from the California Institute of Regenerative Medicine Bridges to Stem Cell Research Program (Pasadena City College and Caltech; M.R.-W.), the L. A. Garfinkle Memorial Laboratory Fund, the Al Sherman Foundation, and the Albert Billings Ruddock Professorship (E.V.R.). Data Availability. ChIP-seq and RNA-seq data have been deposited in the Gene Expression Omnibus (accession no. GSE154304). B.S. and H.H. contributed equally to this work. Author contributions: B.S., H.H., and E.V.R. designed research; B.S., H.H., M.R.-W., W.Z., and K.M. performed research; D.L. and Y.G. contributed new reagents/analytic tools; B.S., H.H., M.R.-W., W.Z., V.R.T., and E.V.R. analyzed data; and B.S., H.H., and E.V.R. wrote the paper with contributions from D.L. and Y.G. Competing interest statement: E.V.R. is a member of the Scientific Advisory Board of Century Therapeutics, LLC. This article is a PNAS Direct Submission. This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2019655118/-/DCSupplemental.

Attached Files

Published - e2019655118.full.pdf

Supplemental Material - pnas.2019655118.sapp.pdf

Supplemental Material - pnas.2019655118.sd01.xlsx

Supplemental Material - pnas.2019655118.sd02.xlsx

Supplemental Material - pnas.2019655118.sd03.xlsx

Supplemental Material - pnas.2019655118.sd04.xlsx

Supplemental Material - pnas.2019655118.sd05.xlsx

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Additional details

Created:
August 22, 2023
Modified:
December 22, 2023