Low-level repressive histone marks fine-tune gene transcription in neural stem cells

  1. Arjun Rajan
  2. Lucas Anhezini
  3. Noemi Rives-Quinto
  4. Jay Yash Chhabra
  5. Megan C Neville
  6. Elizabeth D Larson
  7. Stephen F Goodwin
  8. Melissa M Harrison
  9. Cheng-Yu Lee  Is a corresponding author
  1. University of Michigan-Ann Arbor, United States
  2. University of Oxford, United Kingdom
  3. University of Wisconsin-Madison, United States

Abstract

Coordinated regulation of gene activity by transcriptional and translational mechanisms poise stem cells for a timely cell-state transition during differentiation. Although important for all stemness-to-differentiation transitions, mechanistic understanding of the fine-tuning of gene transcription is lacking due to the compensatory effect of translational control. We used intermediate neural progenitor (INP) identity commitment to define the mechanisms that fine-tune stemness gene transcription in fly neural stem cells (neuroblasts). We demonstrate that the transcription factor FruitlessC (FruC) binds cis-regulatory elements of most genes uniquely transcribed in neuroblasts. Loss of fruC function alone has no effect on INP commitment but drives INP dedifferentiation when translational control is reduced. FruC negatively regulates gene expression by promoting low-level enrichment of the repressive histone mark H3K27me3 in gene cis-regulatory regions. Identical to fruC loss-of-function, reducing Polycomb Repressive Complex 2 activity increases stemness gene activity. We propose low-level H3K27me3 enrichment fine-tunes gene transcription in stem cells, a mechanism likely conserved from flies to humans.

Data availability

Sequencing data have been deposited in GEO under accession codes GSE218257All quantifications are provided in Supplementary File 1.All analysis code used has been deposited in GitHub: https://github.com/Cheng-Yu-Lee-Lab/Rajan-et-al-2023

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

Article and author information

Author details

  1. Arjun Rajan

    Life Sciences Institute, University of Michigan-Ann Arbor, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7043-1031
  2. Lucas Anhezini

    Life Sciences Institute, University of Michigan-Ann Arbor, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Noemi Rives-Quinto

    Life Sciences Institute, University of Michigan-Ann Arbor, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Jay Yash Chhabra

    Life Sciences Institute, University of Michigan-Ann Arbor, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Megan C Neville

    Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8506-9944
  6. Elizabeth D Larson

    Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Stephen F Goodwin

    Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0552-4140
  8. Melissa M Harrison

    Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8228-6836
  9. Cheng-Yu Lee

    Life Sciences Institute, University of Michigan-Ann Arbor, Ann Arbor, United States
    For correspondence
    leecheng@umich.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2291-1297

Funding

National Institute of Neurological Disorders and Stroke (R01NS107496)

  • Cheng-Yu Lee

National Institute of Neurological Disorders and Stroke (R01NS111647)

  • Melissa M Harrison
  • Cheng-Yu Lee

Wellcome Trust (106189/Z/14/Z)

  • Stephen F Goodwin

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

Reviewing Editor

  1. Chris Q Doe, Howard Hughes Medical Institute, University of Oregon, United States

Version history

  1. Preprint posted: November 18, 2022 (view preprint)
  2. Received: January 11, 2023
  3. Accepted: June 11, 2023
  4. Accepted Manuscript published: June 14, 2023 (version 1)
  5. Version of Record published: July 13, 2023 (version 2)

Copyright

© 2023, Rajan 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. Arjun Rajan
  2. Lucas Anhezini
  3. Noemi Rives-Quinto
  4. Jay Yash Chhabra
  5. Megan C Neville
  6. Elizabeth D Larson
  7. Stephen F Goodwin
  8. Melissa M Harrison
  9. Cheng-Yu Lee
(2023)
Low-level repressive histone marks fine-tune gene transcription in neural stem cells
eLife 12:e86127.
https://doi.org/10.7554/eLife.86127

Share this article

https://doi.org/10.7554/eLife.86127

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