The single-cell chromatin accessibility landscape in mouse perinatal testis development

  1. Hoi Ching Suen
  2. Shitao Rao
  3. Alfred Chun Shui Luk
  4. Ruoyu Zhang
  5. Lele Yang
  6. Huayu Qi
  7. Hon Cheong So
  8. Robin M Hobbs  Is a corresponding author
  9. Tin-lap Lee  Is a corresponding author
  10. Jinyue Liao  Is a corresponding author
  1. Chinese University of Hong Kong, Hong Kong
  2. Fujian Medical University, China
  3. Guangzhou Institutes of Biomedicine and Health, China
  4. Hudson Institute of Medical Research, Australia

Abstract

Spermatogenesis depends on an orchestrated series of developing events in germ cells and full maturation of the somatic microenvironment. To date, the majority of efforts to study cellular heterogeneity in testis has been focused on single-cell gene expression rather than the chromatin landscape shaping gene expression. To advance our understanding of the regulatory programs underlying testicular cell types, we analyzed single-cell chromatin accessibility profiles in more than 25,000 cells from mouse developing testis. We showed that scATAC-Seq allowed us to deconvolve distinct cell populations and identify cis-regulatory elements (CREs) underlying cell type specification. We identified sets of transcription factors associated with cell type-specific accessibility, revealing novel regulators of cell fate specification and maintenance. Pseudotime reconstruction revealed detailed regulatory dynamics coordinating the sequential developmental progressions of germ cells and somatic cells. This high-resolution dataset also unveiled previously unreported subpopulations within both the Sertoli and Leydig cell groups. Further, we defined candidate target cell types and genes of several GWAS signals, including those associated with testosterone levels and coronary artery disease. Collectively, our data provide a blueprint of the 'regulon' of the mouse male germline and supporting somatic cells.

Data availability

All raw and processed sequencing data generated in this study have been submitted to the NCBI Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE164439. Code for producing the majority of analyses from this paper is available on GitHub at https://github.com/liaojinyue/mouse_testis_scATAC.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Hoi Ching Suen

    Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, Hong Kong
    Competing interests
    The authors declare that no competing interests exist.
  2. Shitao Rao

    School of Medical Technology and Engineering, Fujian Medical University, Fujian, China
    Competing interests
    The authors declare that no competing interests exist.
  3. Alfred Chun Shui Luk

    Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, Hong Kong
    Competing interests
    The authors declare that no competing interests exist.
  4. Ruoyu Zhang

    Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, Hong Kong
    Competing interests
    The authors declare that no competing interests exist.
  5. Lele Yang

    Guangzhou Regenerative Medicine and Health Bioland Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Huayu Qi

    Guangzhou Regenerative Medicine and Health Bioland Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  7. Hon Cheong So

    Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, Hong Kong
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7102-833X
  8. Robin M Hobbs

    Centre for Reproductive Health, Hudson Institute of Medical Research, Melbourne, Australia
    For correspondence
    robin.hobbs@monash.edu
    Competing interests
    The authors declare that no competing interests exist.
  9. Tin-lap Lee

    Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, Hong Kong
    For correspondence
    tinlaplee@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6654-0988
  10. Jinyue Liao

    Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, Hong Kong
    For correspondence
    Liaojinyue@cuhk.edu.hk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3392-3760

Funding

Chinese University of Hong Kong (Department of Chemical Pathology's Faculty Startup Fund)

  • Jinyue Liao

University Grants Committee (General Research Fund CUHK 14120418)

  • Tin-lap Lee

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

Reviewing Editor

  1. Deborah Bourc'his, Institut Curie, France

Ethics

Animal experimentation: All the animal experiments were performed according to the protocols approved by the Animal Experiment Ethics Committee (AEEC) of The Chinese University of Hong Kong (CUHK) and followed the Animals (Control of Experiments) Ordinance (Cap. 340) licensed from the Department of Health, the Government of Hong Kong Special Administrative Region.

Version history

  1. Preprint posted: March 17, 2021 (view preprint)
  2. Received: November 16, 2021
  3. Accepted: April 24, 2023
  4. Accepted Manuscript published: April 25, 2023 (version 1)
  5. Accepted Manuscript updated: April 27, 2023 (version 2)
  6. Version of Record published: May 11, 2023 (version 3)

Copyright

© 2023, Suen 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. Hoi Ching Suen
  2. Shitao Rao
  3. Alfred Chun Shui Luk
  4. Ruoyu Zhang
  5. Lele Yang
  6. Huayu Qi
  7. Hon Cheong So
  8. Robin M Hobbs
  9. Tin-lap Lee
  10. Jinyue Liao
(2023)
The single-cell chromatin accessibility landscape in mouse perinatal testis development
eLife 12:e75624.
https://doi.org/10.7554/eLife.75624

Share this article

https://doi.org/10.7554/eLife.75624

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