Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo

  1. Dennis May
  2. Sangwon Yun
  3. David G Gonzalez
  4. Sangbum Park
  5. Yanbo Chen
  6. Elizabeth Lathrop
  7. Biao Cai
  8. Tianchi Xin
  9. Hongyu Zhao
  10. Siyuan Wang
  11. Lauren E Gonzalez  Is a corresponding author
  12. Katie Cockburn  Is a corresponding author
  13. Valentina Greco  Is a corresponding author
  1. Yale University, United States
  2. Michigan State University, United States
  3. McGill University, Canada

Abstract

Stem cell differentiation requires dramatic changes in gene expression and global remodeling of chromatin architecture. How and when chromatin remodels relative to the transcriptional, behavioral, and morphological changes during differentiation remain unclear, particularly in an intact tissue context. Here, we develop a quantitative pipeline which leverages fluorescently-tagged histones and longitudinal imaging to track large-scale chromatin compaction changes within individual cells in a live mouse. Applying this pipeline to epidermal stem cells, we reveal that cell-to-cell chromatin compaction heterogeneity within the stem cell compartment emerges independent of cell cycle status, and instead is reflective of differentiation status. Chromatin compaction state gradually transitions over days as differentiating cells exit the stem cell compartment. Moreover, establishing live imaging of Keratin-10 (K10) nascent RNA, which marks the onset of stem cell differentiation, we find that Keratin-10 transcription is highly dynamic and largely precedes the global chromatin compaction changes associated with differentiation. Together, these analyses reveal that stem cell differentiation involves dynamic transcriptional states and gradual chromatin rearrangement.

Data availability

All coding scripts and source datasheets for figure quantifications are made accessible through the Dryad data repository: https://doi.org/10.5061/dryad.5hqbzkh94. Representative raw imaging data are accessible through the same link and full datasets available upon request with no restrictions (due to size) by contacting VG. Source datasheets are included in supplemental information.

Article and author information

Author details

  1. Dennis May

    Department of Genetics, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Sangwon Yun

    Department of Genetics, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. David G Gonzalez

    Department of Genetics, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Sangbum Park

    Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Yanbo Chen

    Department of Genetics, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Elizabeth Lathrop

    Department of Genetics, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Biao Cai

    Department of Biostatistics, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Tianchi Xin

    Department of Genetics, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Hongyu Zhao

    Department of Biostatistics, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Siyuan Wang

    Department of Genetics, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6550-4064
  11. Lauren E Gonzalez

    Department of Genetics, Yale University, New Haven, United States
    For correspondence
    lauren.e.gonzalez@yale.edu
    Competing interests
    The authors declare that no competing interests exist.
  12. Katie Cockburn

    Department of Biochemistry, McGill University, Montreal, Canada
    For correspondence
    katie.cockburn@mcgill.ca
    Competing interests
    The authors declare that no competing interests exist.
  13. Valentina Greco

    Department of Genetics, Yale University, New Haven, United States
    For correspondence
    valentina.greco@yale.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6492-4603

Funding

National Institute of Arthritis and Musculoskeletal and Skin Diseases (1R01AR063663-01)

  • Valentina Greco

National Institute of Arthritis and Musculoskeletal and Skin Diseases (1R01AR067755-01A1)

  • Valentina Greco

National Institute on Aging (1DP1AG066590-01)

  • Valentina Greco

National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01AR072668)

  • Valentina Greco

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Melike Lakadamyali, University of Pennsylvania, United States

Ethics

Animal experimentation: All procedures involving animal subjects were performed under the approval of the Institutional Animal Care and Use Committee (IACUC) of the Yale School of Medicine (Protocol #2021-11303). All live imaging was performed under 1-2% isoflurane, and ever effort was made to minimize suffering.

Version history

  1. Received: September 13, 2022
  2. Preprint posted: October 7, 2022 (view preprint)
  3. Accepted: March 6, 2023
  4. Accepted Manuscript published: March 7, 2023 (version 1)
  5. Version of Record published: March 20, 2023 (version 2)

Copyright

© 2023, May et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Dennis May
  2. Sangwon Yun
  3. David G Gonzalez
  4. Sangbum Park
  5. Yanbo Chen
  6. Elizabeth Lathrop
  7. Biao Cai
  8. Tianchi Xin
  9. Hongyu Zhao
  10. Siyuan Wang
  11. Lauren E Gonzalez
  12. Katie Cockburn
  13. Valentina Greco
(2023)
Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo
eLife 12:e83444.
https://doi.org/10.7554/eLife.83444

Share this article

https://doi.org/10.7554/eLife.83444

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