Bidirectional regulation of postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamics
- Duke University, United States
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.
-
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellumNCBI Gene Expression Omnibus, GSE60731.
Article and author information
Author details
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.
Ethics
Animal experimentation: We performed all procedures under an approved protocol from the Duke University Institutional Animal Care and Use Committee, (#A035-20-02).
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.
Metrics
-
- 2,047
- views
-
- 245
- downloads
-
- 16
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
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)
Bidirectional regulation of postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamics
eLife 12:e86273.
https://doi.org/10.7554/eLife.86273
Further reading
-
- Chromosomes and Gene Expression
RNA interference (RNAi) is a conserved pathway that utilizes Argonaute proteins and their associated small RNAs to exert gene regulatory function on complementary transcripts. While the majority of germline-expressed RNAi proteins reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here, we find that the small RNA biogenesis machinery is spatially and temporally organized during Caenorhabditis elegans embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we further demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.
-
- Chromosomes and Gene Expression
- Genetics and Genomics
A new method for mapping torsion provides insights into the ways that the genome responds to the torsion generated by RNA polymerase II.
