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.
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.
Bidirectional changes in postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamicsNCBI Gene Expression Omnibus, GSE212441.
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellumNCBI Gene Expression Omnibus, GSE60731.
Promoter Decommissioning by the NuRD Chromatin Remodeling Complex Triggers Synaptic Connectivity in the Mammalian BrainExpression Omnibus, GSE57758.
Sensory experience remodels genome architecture in neural circuit to drive motor learningExpression Omnibus, GSE127995.
- Anne E West
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Animal experimentation: We performed all procedures under an approved protocol from the Duke University Institutional Animal Care and Use Committee, (#A035-20-02).
- Gail Mandel, Oregon Health and Science University, United States
© 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.
The cohesin complex plays essential roles in chromosome segregation, 3D genome organisation, and DNA damage repair through its ability to modify DNA topology. In higher eukaryotes, meiotic chromosome function, and therefore fertility, requires cohesin complexes containing meiosis-specific kleisin subunits: REC8 and RAD21L in mammals and REC-8 and COH-3/4 in Caenorhabditis elegans. How these complexes perform the multiple functions of cohesin during meiosis and whether this involves different modes of DNA binding or dynamic association with chromosomes is poorly understood. Combining time-resolved methods of protein removal with live imaging and exploiting the temporospatial organisation of the C. elegans germline, we show that REC-8 complexes provide sister chromatid cohesion (SCC) and DNA repair, while COH-3/4 complexes control higher-order chromosome structure. High-abundance COH-3/4 complexes associate dynamically with individual chromatids in a manner dependent on cohesin loading (SCC-2) and removal (WAPL-1) factors. In contrast, low-abundance REC-8 complexes associate stably with chromosomes, tethering sister chromatids from S-phase until the meiotic divisions. Our results reveal that kleisin identity determines the function of meiotic cohesin by controlling the mode and regulation of cohesin–DNA association, and are consistent with a model in which SCC and DNA looping are performed by variant cohesin complexes that coexist on chromosomes.
Though long non-coding RNAs (lncRNAs) represent a substantial fraction of the Pol II transcripts in multicellular animals, only a few have known functions. Here we report that the blocking activity of the Bithorax complex (BX-C) Fub-1 boundary is segmentally regulated by its own lncRNA. The Fub-1 boundary is located between the Ultrabithorax (Ubx) gene and the bxd/pbx regulatory domain, which is responsible for regulating Ubx expression in parasegment PS6/segment A1. Fub-1 consists of two hypersensitive sites, HS1 and HS2. HS1 is an insulator while HS2 functions primarily as an lncRNA promoter. To activate Ubx expression in PS6/A1, enhancers in the bxd/pbx domain must be able to bypass Fub-1 blocking activity. We show that the expression of the Fub-1 lncRNAs in PS6/A1 from the HS2 promoter inactivates Fub-1 insulating activity. Inactivation is due to read-through as the HS2 promoter must be directed toward HS1 to disrupt blocking.