Bidirectional regulation of postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamics

Abstract

The functional maturation of neurons is a prolonged process that extends past mitotic exit and is mediated by the chromatin-dependent orchestration of gene transcription programs. We find that expression of this maturation gene program in mouse cerebellar granule neurons (CGNs) requires dynamic changes in the genomic distribution of histone H3 lysine 27 trimethylation (H3K27me3), demonstrating a function for this chromatin modification beyond its role in cell fate specification. The developmental loss of H3K27me3 at promoters of genes activated as CGNs mature is facilitated by the lysine demethylase and ASD-risk gene, Kdm6b. Interestingly, inhibition of the H3K27 methyltransferase EZH2 in newborn CGNs not only blocks the repression of progenitor genes but also impairs the induction of mature CGN genes, showing the importance of bidirectional H3K27me3 regulation across the genome. These data demonstrate that H3K27me3 turnover in developing postmitotic neurons regulates the temporal coordination of gene expression programs that underlie functional neuronal maturation.

Data availability

H3K27me3 ChIP-seq data for P7, P14 and P60 cerebellum, WT and Kdm6b-cKO cerebellum; RNA-seq data for WT and Kdm6b-cKO cerebellum; CUT&RUN and RNA-seq data for cultured CGNs can be accessed at GEO: GSE212441.RNA-seq data for P7, P14 and P60 cerebellum and DIV0 and DIV7 CGNs, H3K27ac, ZIC1/2 ChIP-seq data and DHS-seq data for P7 and P60 cerebellum were adapted from Frank et. al 2015 (PMID: 25849986)H3K4me3 ChIP-seq data from P6 and P22 cerebellum were obtained and adapted from (Yamada et al., 2014) and can be accessed at GEO: GSE57758. H3K4me1 ChIP-seq data from P9 cerebellum was obtained and adapted from (Ramirez et al., 2022) and can be accessed at GEO: GSE183697. H3K4me3 PLAC-seq tracks were obtained from (Yamada et al., 2019) and can be accessed at GEO: GSE127995.Source data files for western blots in Figure 1, 7, S1 and S9 are included in Supplemental Files.Primers used to perform RT-qPCR have been provided in Table S1.DESeq2-normalized counts used to generate heatmaps in the study have been provided in Table S2.Gene lists used for Gene Ontology analyses have been provided in Table S3.Tables S1, S3 and S3 are included in Supplemental Files.

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

Article and author information

Author details

  1. Vijyendra Ramesh

    Molecular Cancer Biology Program, Duke University, Durham, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8818-6863
  2. Fang Liu

    Department of Neurobiology, Duke University, Durham, United States
    Competing interests
    No competing interests declared.
  3. Melyssa S Minto

    Department of Neurobiology, Duke University, Durham, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5438-7285
  4. Urann Chan

    Department of Neurobiology, Duke University, Durham, United States
    Competing interests
    No competing interests declared.
  5. Anne E West

    Molecular Cancer Biology Program, Duke University, Durham, United States
    For correspondence
    west@neuro.duke.edu
    Competing interests
    Anne E West, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0846-139X

Funding

National Institutes of Health (R01NS0988804)

  • Anne E West

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

Reviewing Editor

  1. Gail Mandel, Oregon Health and Science University, United States

Ethics

Animal experimentation: We performed all procedures under an approved protocol from the Duke University Institutional Animal Care and Use Committee, (#A035-20-02).

Version history

  1. Preprint posted: October 10, 2022 (view preprint)
  2. Received: January 18, 2023
  3. Accepted: April 21, 2023
  4. Accepted Manuscript published: April 24, 2023 (version 1)
  5. Version of Record published: May 12, 2023 (version 2)

Copyright

© 2023, Ramesh 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. Vijyendra Ramesh
  2. Fang Liu
  3. Melyssa S Minto
  4. Urann Chan
  5. Anne E West
(2023)
Bidirectional regulation of postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamics
eLife 12:e86273.
https://doi.org/10.7554/eLife.86273

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https://doi.org/10.7554/eLife.86273

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