Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1

  1. Hsin-I Jen
  2. Matthew C Hill
  3. Litao Tao
  4. Kuanwei Sheng
  5. Wenjian Cao
  6. Hongyuan Zhang
  7. Haoze V Yu
  8. Juan Llamas
  9. Chenghang Zong
  10. James F Martin
  11. Neil Segil
  12. Andrew K Groves  Is a corresponding author
  1. Baylor College of Medicine, United States
  2. University of Southern California, United States

Abstract

The mammalian cochlea loses its ability to regenerate new hair cells prior to the onset of hearing. In contrast, the adult vestibular system can produce new hair cells in response to damage, or by reprogramming of supporting cells with the hair cell transcription factor Atoh1. We used RNA-seq and ATAC-seq to probe the transcriptional and epigenetic responses of utricle supporting cells to damage and Atoh1 transduction. We show that the improved regenerative response of the utricle correlates with a more accessible chromatin structure in utricle supporting cells compared to their cochlear counterparts. We also provide evidence that Atoh1 transduction of supporting cells is able to promote increased transcriptional accessibility of some hair cell genes. Our study offers a possible explanation for regenerative differences between sensory organs of the inner ear, but shows that additional factors to Atoh1 may be required for optimal reprogramming of hair cell fate.

Data availability

Sequencing data have been deposited in GEO under accession codes GSE122732 and GSE121610

The following data sets were generated

Article and author information

Author details

  1. Hsin-I Jen

    Program in Developmental Biology, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Matthew C Hill

    Program in Developmental Biology, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Litao Tao

    Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Kuanwei Sheng

    Program Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Wenjian Cao

    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Hongyuan Zhang

    Department of Neuroscience, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Haoze V Yu

    Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Juan Llamas

    Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Chenghang Zong

    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. James F Martin

    Program in Developmental Biology, Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Neil Segil

    Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Andrew K Groves

    Program in Developmental Biology, Baylor College of Medicine, Houston, United States
    For correspondence
    akgroves@bcm.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0784-7998

Funding

National Cancer Institute (CA125123)

  • Andrew K Groves

Vivian L Smith Foundation and MacDonald Research Fund Award (16RDM001)

  • James F Martin

Transatlantic Network of Excellence Award LeDucq Foundation Transatlantic Networks of Excellence in Cardiovascular Research (14CVD01)

  • James F Martin

National Institute on Deafness and Other Communication Disorders (RO1DC014832)

  • Andrew K Groves

National Institute on Deafness and Other Communication Disorders (RO1DC015829)

  • Neil Segil

Eunice Kennedy Shriver National Institute of Child Health and Human Development (RO1DE023177)

  • James F Martin

National Heart, Lung, and Blood Institute (RO1HL127717)

  • James F Martin

National Heart, Lung, and Blood Institute (RO1HL130804)

  • James F Martin

National Heart, Lung, and Blood Institute (RO1HL118761)

  • James F Martin

National Institutes of Health (DP2EB020399)

  • Chenghang Zong

National Heart, Lung, and Blood Institute (F31HL136065)

  • Matthew C Hill

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

Ethics

Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols (AN-4956) of Baylor College of Medicine

Reviewing Editor

  1. Francois Guillemot, The Francis Crick Institute, United Kingdom

Publication history

  1. Received: December 12, 2018
  2. Accepted: April 28, 2019
  3. Accepted Manuscript published: April 29, 2019 (version 1)
  4. Version of Record published: May 7, 2019 (version 2)

Copyright

© 2019, Jen 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.

Metrics

  • 4,492
    Page views
  • 620
    Downloads
  • 29
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Hsin-I Jen
  2. Matthew C Hill
  3. Litao Tao
  4. Kuanwei Sheng
  5. Wenjian Cao
  6. Hongyuan Zhang
  7. Haoze V Yu
  8. Juan Llamas
  9. Chenghang Zong
  10. James F Martin
  11. Neil Segil
  12. Andrew K Groves
(2019)
Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1
eLife 8:e44328.
https://doi.org/10.7554/eLife.44328

Further reading

    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine
    Marta Perera et al.
    Research Article

    During embryonic development cells acquire identity at the same time as they are proliferating, implying that an intrinsic facet of cell fate choice requires coupling lineage decisions to rates of cell division. How is the cell cycle regulated to promote or suppress heterogeneity and differentiation? We explore this question combining time lapse imaging with single cell RNA-seq in the contexts of self-renewal, priming and differentiation of mouse embryonic stem cells (ESCs) towards the Primitive Endoderm lineage (PrE). Since ESCs are derived from the Inner Cell Mass of the mammalian blastocyst, ESCs in standard culture conditions are transcriptionally heterogeneous containing subfractions that are primed for either of the two ICM lineages, Epiblast and PrE. These subfractions represent dynamic states that can readily interconvert in culture, and the PrE subfraction is functionally primed for endoderm differentiation. Here we find that differential regulation of cell cycle can tip the balance between these primed populations, such that naïve ESC culture conditions promote Epiblast-like expansion and PrE differentiation stimulates the selective survival and proliferation of PrE-primed cells. In endoderm differentiation, we find that this change is accompanied by a counter-intuitive increase in G1 length that also appears replicated in vivo. While FGF/ERK signalling is a known key regulator of ESCs and PrE differentiation, we find it is not just responsible for ESCs heterogeneity, but also cell cycle synchronisation, required for the inheritance of similar cell cycles between sisters and cousins. Taken together, our results point to a tight relationship between transcriptional heterogeneity and cell cycle regulation in the context of lineage priming, with primed cell populations providing a pool of flexible cell types that can be expanded in a lineage-specific fashion while allowing plasticity during early determination.

    1. Cell Biology
    2. Developmental Biology
    Swathy Babu et al.
    Research Article

    Btg3-associated nuclear protein (Banp) was originally identified as a nuclear matrix-associated region (MAR)-binding protein and it functions as a tumor suppressor. At the molecular level, Banp regulates transcription of metabolic genes via a CGCG-containing motif called the Banp motif. However, its physiological roles in embryonic development are unknown. Here, we report that Banp is indispensable for the DNA damage response and chromosome segregation during mitosis. Zebrafish banp mutants show mitotic cell accumulation and apoptosis in developing retina. We found that DNA replication stress and tp53-dependent DNA damage responses were activated to induce apoptosis in banp mutants, suggesting that Banp is required for regulation of DNA replication and DNA damage repair. Furthermore, consistent with mitotic cell accumulation, chromosome segregation was not smoothly processed from prometaphase to anaphase in banp morphants, leading to a prolonged M-phase. Our RNA- and ATAC-sequencing identified 31 candidates for direct Banp target genes that carry the Banp motif. Interestingly, a DNA replication fork regulator, wrnip1, and two chromosome segregation regulators, cenpt and ncapg, are included in this list. Thus, Banp directly regulates transcription of wrnip1 for recovery from DNA replication stress, and cenpt and ncapg for chromosome segregation during mitosis. Our findings provide the first in vivo evidence that Banp is required for cell-cycle progression and cell survival by regulating DNA damage responses and chromosome segregation during mitosis.