Rapid cellular responses to environmental stimuli are fundamental for development and maturation. Immediate early genes can be transcriptionally induced within minutes in response to a variety of signals. How their induction levels are regulated and their untimely activation by spurious signals prevented during development is poorly understood. We found that in developing sensory neurons, before perinatal sensory-activity-dependent induction, immediate early genes are embedded into a unique bipartite Polycomb chromatin signature, carrying active H3K27ac on promoters but repressive Ezh2-dependent H3K27me3 on gene bodies. This bipartite signature is widely present in developing cell types, including embryonic stem cells. Polycomb marking of gene bodies inhibits mRNA elongation, dampening productive transcription, while still allowing for fast stimulus-dependent mark removal and bipartite gene induction. We reveal a developmental epigenetic mechanism regulating the rapidity and amplitude of the transcriptional response to relevant stimuli, while preventing inappropriate activation of stimulus-response genes.
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All raw sequencing data and processed data used for this study are available through ArrayExpress and will be released to the public without restrictions: mRNA-seq (Smart-seq2), E-MTAB-8314; total RNA-seq (Solo RNA-seq), E-MTAB-8311; ChIP–seq (ChIPmentation), E-MTAB-8317; ATAC–seq, E-MTAB-8313; 4C–seq, E-MTAB-8295; and single-cell RNA-seq (10x Genomics), E-MTAB-8312. FACS gating strategies/source data are presented in Supplementary Figs. 1–4. Public sequencing datasets were obtained from the Gene Expression Omnibus and ENCODE as follows: mouse cortical culture (GSE21161 and GSE60192), mouse embryonic forebrain (GSE93011 and GSE52386), mouse adult cortical excitatory neuron (GSE63137), mouse ESCs (GSE36114 and GSE94250), mouse ESCs for Ezh2-KO experiments (GSE116603), mouse E14.5 heart tissues (GSE82764, GSE82637, GSE82640 and GSE78441; ENCSR068YGC), mouse E14.5 liver tissues (GSE78422, GSE82407, GSE82615 and GSE82620; ENCSR032HKE) and E10.5 mouse NCCs isolated from the frontal nasal process (GSE89437).
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F.M.R. wishes to dedicate this paper to the memory of P. Sassone-Corsi (1956–2020), dear friend and eminent scientist who made seminal contributions to immediate early gene and activator protein-1 transcriptional regulation and with whom F.M.R. discussed this project at an early stage. We thank A. Pombo for very useful discussion. We thank N. Vilain, S. Smallwood, D. Gaidatzis and the members of the Rijli group and FMI facilities for excellent technical support and discussion. We thank S. H. Orkin (Harvard Medical School) and A. Wutz (ETH Zurich) for the kind gifts of the Ezh2flox mouse line and EedKO ESCs, respectively. The LAL-R26TVA-LacZ line was a kind gift from D. Saur (Technische Universitat Munchen). T.K. was supported by a Japan Society for the Promotion of Science fellowship, and O.J. was supported by an EMBO Long-Term fellowship. F.M.R. was supported by the Swiss National Science Foundation (31003A_149573 and 31003A_175776). This project has also received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant no. 810111-EpiCrest2Reg). F.M.R. and M.B.S. were also supported by the Novartis Research Foundation.
The authors declare no competing interests.
Peer review information Nature Genetics thanks the anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended Data Fig. 1 Genetic strategy of barrelette neuron isolation and identification of activity response genes.
a and b, Representative FACS gating for barrelette neurons (Supplementary Figs. 1–4). c and d, Intersectional strategies to FACS isolate E14.5, E18.5 or P4 postmitotic barrelette neurons (Drg11vPrV-ZsGreen/+ (c), Drg11vPrV-tdTomato/+ (d)) from ventral principal trigeminal nucleus (vPrV). (Supplementary Table 1, Supplementary Note). e, Intersectional strategy to FACS isolate Kir2.1(Kir)-mCherry overexpressing, neuronal activity-deprived, vPrV barrelette neurons (Drg11vPrV-Kir/+; Supplementary Table 1, Supplementary Note). f, Volumes of PrV in control (K20tdTomato/+;r2EGFP/+) and Kir overexpressing (K20Kir/+;r2EGFP/+) mice (n = 3, biologically independent animals). g and h, P8 cytochrome oxidase (CO) staining in wild-type (WT; g) and K20Kir/+ (h) mice. Representative images of n = 3 biologically independent animals. Scale bars: 200 μm. i–p, P10 barrelette neuron dendrite orientation by GFP expression after pseudotyped rabies virus (EnvA-SADΔG-GFP) injection in P3 thalamus in control Krox20::Cre;LSL-R26TVA-LacZ (K20TVA/+) (j) and Kir overexpressing Krox20::Cre;R26Kir-mCherry;LSL-R26TVA-LacZ (K20TVA/Kir) (k) mice. Scale bars: 10 μm. Symmetry index (l) and surface ratio (p) are compared (Supplementary Methods). n = 8 (K20TVA/+) and n = 6 (K20TVA/Kir) biologically independent animals were used, and j, k, n, o are representative images. q and r, MA-plots comparing E18.5 and E14.5 mRNA levels in control Drg11vPrV-ZsGreen/+ barrelette neurons (q), and E18.5 Drg11vPrV-Kir/+ (Kir-OE) and E18.5 Drg11vPrV-ZsGreen/+ wild-type (WT) barrelette neurons (r). 702 genes (green dots, q) increase their expression at E18.5 as compared to E14.5 (log2(fold change) > 1.5), while 102 genes (red dots, r) decrease their expression in E18.5 Kir-OE barrelette neurons (log2(fold change) < –1) (Methods). s, Identification of 56 bsARGs. t, Fractions of the 56 bsARGs (left) and 83 nbARGs (right) with H3K27me3- and H3K27me3+ profiles in E14.5 Drg11vPrV-ZsGreen/+ barrelette neurons (see Fig. 1c). u, Scatterplots showing ATAC–seq (x axis) and H3K4me2 (y axis) signals on promoters (1 kb around TSS) in E14.5 Drg11vPrV-ZsGreen/+ barrelette neurons. Dashed lines indicate thresholds corresponding to a 5% false discovery rate (FDR) (Methods) (see Fig. 1c). f, l, p, Bars indicate median and P values are from Welch’s two-sample two-sided t-tests. NS: not significant (P > 0.05).
a, Fos, Egr1, Fosb and Nr4a3 genome browser views. ATAC (violet), H3K4me2 (yellow, E14.5 barrelette neurons), H3K4me3 (yellow, adult cortical neurons and cultured embryonic neurons), H3K27ac (red) and H3K27me3 (blue) are shown in E14.5 Drg11vPrV-ZsGreen/+ barrelette neurons, E15.5 embryonic cortical neural progenitors (NPC) and postmitotic neurons (PMID: 28793256), adult cortical excitatory neurons (PMID: 26087164), and embryonic cortical 7 day ex vivo cultured neurons (PMID: 20393465). Shaded boxes highlight promoters (pink) and gene bodies (blue). IEGs display a bipartite chromatin signature characterized by promoter-H3K27ac and gene body-H3K27me3 in E14.5 barrelette neurons and E15.5 cortical progenitors and postmitotic neurons. In contrast, H3K27me3 is not present on IEG gene bodies in postnatal cortical excitatory neurons, similar to postnatal barrelette neurons (see Fig. 3e and Extended Data Fig. 6b). Also, culturing embryonic cortical neurons for one week results in depletion of the H3K27me3 mark, similar to embryonic hindbrain neuron culture (see Extended Data Fig. 9a). In long genes (for example Nr4a3), H3K27me3 deposition on gene body does not stretch throughout the gene body, but is restricted only to the proximal region downstream of the promoter (also see Extended Data Fig. 3c). b, IEG (Fos, Egr1 and Fosb) genome browser views at E14.5, pre-fixed prior to the dissociation procedure. Shaded boxes highlight promoters (pink) and gene bodies (blue). The presence of the bipartite pattern (H3K27ac + promoter/H3K27me3+ gene body) in the pre-fixed tissue indicates that it is not induced by the dissociation procedure.
a and b, Bipartite (a) and bivalent (b) gene rank (x axis) and corresponding rate of correct bipartite and bivalent classification obtained through genome browser visual inspection of individual loci (y axis, fraction of bipartite true-positive, Methods) in E10.5 K20tdTomato/+ progenitors and E14.5, E18.5 and P4 Drg11vPrV-ZsGreen/+ barrelette neurons. c, Aggregate plot showing profile of H3K27me3 around the transcription start site (TSS) in E14.5Bip genes (top 100 genes ranked by bipartiteness scores in E14.5 Drg11vPrV-ZsGreen/+ barrelette neurons) with long gene length (>10 kb). Promoters (defined as 1 kb upstream to 500 bp downstream of TSS) and gene bodies (from 1 kb to 3 kb downstream of TSS) are highlighted. Note that H3K27me3 on gene bodies does not stretch further than 2-3 kb downstream of the TSS, even when genes are long. d, Genome browser profiles of representative bipartite IEGs (Fos, Egr1) in mouse ESCs. Note that the H3K27me3 mark is deposited not only on downstream (gene body) but also upstream regions of these H3K27ac promoters. e, Scatterplots showing promoter H3K27ac (x axis) and gene body H3K27me3 (y axis) signals in E14.5 rhombomere 3 (r3)-derived K20tdTomato/+ hindbrain cells. E14.5Bip genes identified in Drg11vPrV-ZsGreen/+ barrelette neurons are mapped (red dots). Dashed lines indicate thresholds corresponding to a 5% false discovery rate (FDR) based on a gaussian mixture model with two components (for foreground and background, see Methods). Barrelette neuron E14.5Bip genes show high levels of promoter H3K27ac and gene body H3K27me3 indicating that they are bipartite also in r3-derived K20tdTomato/+ hindbrain cells. f, CpG average observed/expected (o/e) ratios in a 100 bp window in E14.5Bip and E14.5Biv gene loci. Bins overlapping with the promoter, TSS, and gene body are indicated. g, Transcription factor binding motifs specifically enriched in E14.5Bip as compared to E14.5Biv promoters (Methods).
Extended Data Fig. 4 Coexistence of H3K27ac and H3K27me3 at promoter and gene body of bipartite genes.
a, Scheme of sequential ChIP-seq protocol (Supplementary Methods). b and c, Scatterplots comparing H3K27ac (x axis) and H3K27me3 (y axis) signals detected in regions from −1 kb to +3 kb around the transcription start site (TSS) by single ChIP-seq performed with large (2-3 kb) chromatin fragments in E14.5 hindbrain tissue. The colors indicate the corresponding H3K27me3/H3K27ac sequential-ChIP-seq signals, either for all autosomal genes (b), or only for E14.5Bip genes (c). Dashed lines indicate thresholds corresponding to a 5% FDR based on a gaussian mixture model with two components (for foreground and background, see Methods). Stratified by one single ChIP signal (for example H3K27ac), the sequential ChIP signal still correlates with the other (for example H3K27me3), which indicates that single chromatin fragments have been double-marked and thus have been enriched at both steps of the sequential ChIP experiments. d, Genome browser view of bipartite Egr1 gene locus displaying chromatin accessibility (ATAC-seq), 2-3kb-fragment H3K27ac, H3K27me3 and H3K27me3/H3K27ac sequential-ChIP-seq in E14.5 hindbrain tissue. H3K27me3 and H3K27ac coexist on gene body and promoter, respectively. e, Violin plots displaying promoter H3K27ac (left), bulk mRNA-seq (middle, Smart-seq2), and single cell fraction with detected mRNA-seq (right, 10X genomics) of E10.5 K20tdTomato/+ progenitors. E10.5 bipartite (E10.5Bip) genes (green, n = 99 genes, see Methods) and E10.5 non-bipartite genes with Bip-matching promoter H3K27ac levels (blue, n = 99 genes) are compared. E10.5Bip gene transcripts are only detected in as little as 6% of single cells on average. Plots extend from the data minima to the maxima with the white dot indicating median, the box showing the interquartile range and whiskers extending to the most extreme data point within 1.5X the interquartile range. P values are from two-sided Wilcoxon’s tests. NS: not significant (P > 0.05).
a, Aggregate plot of chromatin profiles (ATAC-seq, ChIP-seq) around transcript start sites (TSSs) of all autosomal genes in E14.5 Drg11vPrV-ZsGreen/+ barrelette neurons. Promoter and gene body regions are highlighted (Methods). b-d, Two-dimensional (2D) projection on a E14.5, E18.5 and P4-combined t-SNE map of autosomal genes according to chromatin accessibility, H3K27me3, H3K4me2, and H3K27ac levels at promoters and gene bodies in Drg11vPrV-ZsGreen/+ barrelette neurons (Methods). b, E14.5 (red), E18.5 (blue) and P4 (green) genes are indicated (Supplementary Note). c, Color-coded t-SNE gene maps according to promoter (top row) and gene body (bottom row) chromatin profiles (columns). d, Color-coded t-SNE gene maps indicating mRNA levels. Numbers 1–3: example genes in E14.5 barrelette neurons. e, Chromatin profiles of the example genes in d, namely H3K4me2 + /H3K27ac + /H3K27me3-/ATAC + (active, Actb), Polycomb-dependent H3K4me2 + /H3K27ac-/H3K27me3 + /ATAC + (permissive, Dlx5) and H3K4me2-/H3K27ac-/H3K27me3-/ATAC- (repressed, Olfr67). f, color-coded E14.5, E18.5 and P4-combined t-SNE gene maps displaying bipartiteness (left) or bivalency (right) scores in E14.5, E18.5 and P4 barrelette neurons (Methods). g, E14.5, E18.5 and P4-combined t-SNE map with contour lines indicating regions enriched with bipartite (green) and bivalent (red) genes (Methods). h, E14.5, E18.5 and P4-combined t-SNE map in which all E14.5 genes are colored according to their developmental change of chromatin state from E14.5 to P4 (Supplementary Note and Methods). i, E14.5Bip genes are subdivided into two subgroups according to their localization on the t-SNE plot (n = 57, E14.5Bip-a genes, orange dots; n = 43, E14.5Bip-b genes, blue dots). j, Violin plots showing promoter H3K27ac (left), gene body H3K27me3 (middle) and mRNA (right) levels in E14.5Bip-a (orange) and E14.5Bip-b genes (blue) in E14.5 barrelette neurons (Supplementary Note and Methods). Plots extend from the data minima to the maxima with the white dot indicating median, the box showing the interquartile range and whiskers extending to the most extreme data point within 1.5X the interquartile range. P values are from two-sided Wilcoxon’s tests. k and l, E10.5 K20tdTomato/+ progenitor t-SNE maps with bipartiteness or bivalency scores (k) and contour lines (l) at E10.5 (Methods).
a, Developmental dynamics of chromatin profiles (ATAC-seq and ChIP-seq signals in promoter and gene body regions) and mRNA levels of E14.5Bip genes in E14.5, E18.5 and P4 Drg11vPrV-ZsGreen/+ barrelette neurons. Log2 fold changes are calculated with reference to E14.5. At P4, 20% of E14.5Bip genes become expressed (Exp, that is RPKM > = 3 at P4), 25% become bivalent (Biv, red dots in Fig. 3d), and the rest (55%) remain bipartite (Bip), (blue, red and green lines, respectively). Bottom: summary diagram. b, Genome browser view of the Egr1 locus at the E10.5, E14.5, E18.5 and P4 stages. c, 3D interaction map (4C-seq) using the Fos promoter (top left), enhancer 2 (e2, bottom left) and enhancer 5 (e5, bottom right) as viewpoints in E10.5, E14.5, E18.5 and P4 hindbrain tissue. Normalized read per 4 C fragment is visualized. d, Genome browser views of Fos and Egr1 at the E14.5, E18.5 and P4 stages. e, Violin plots showing transcription end site (TES, Methods) RNAPII-S7P (left), RNAPII-S2P (middle), and H3K36me3 (right) levels of E14.5Bip genes at E14.5 and P4 (see a). E14.5Bip genes that become expressed (Exp, blue, n = 25) at P4 displayed significantly higher levels of RNAPII-S7P, -S2P and H3K36me3 marks as compared to E14.5Bip genes that become bivalent (Biv, red, n = 20) or remain bipartite (Bip, green, n = 55) at P4: violin deviations between groups are to be compared within the same time point since the time points reflect different batches. Plots extend from the data minima to the maxima with the white dot indicating median, the box showing the interquartile range and whiskers extending to the most extreme data point within 1.5X the interquartile range. P values are from two-sided Wilcoxon’s tests. NS: not significant (P > 0.05).
a, Spliced transcript expression (transcripts per million, TPM, Methods) of E14.5Bip genes (red) and control genes (blue) with matching distributions of spliced transcripts (Methods) (n = 3 biologically independent replicates). b, Unspliced over total transcript fractions for each gene set in a (Methods). Note the larger fraction of unspliced transcripts of E14.5Bip genes compared to control genes. c, Fractions of spliced over total transcripts of E14.5Bip genes (red) in E14.5 control K20tdTomato/+ (WT) and Ezh2cKOr3-RFP hindbrain cells (n = 3, biologically independent littermates). d, Violin plots comparing the TSS/whole gene ratios of total RNA-seq reads between Ezh2cKOr3-RFP and WT hindbrain cells (see Fig. 5c). e, Scatter plot (left) comparing H3K36me3 levels on the coding region between E14.5 wild-type Hoxa2tdTomato/+ (WT) and Ezh2cKOHB-RFP hindbrain cells, indicating H3K36me3-positive and negative E14.5Bip genes in red and gray, respectively (Methods). Increased H3K36me3 levels of H3K36me3-positive E14.5Bip genes in Ezh2-depleted cells are further illustrated (right panel). Bars indicate the median. f, (left, middle) Genes with non-zero expression in EedKO and wild-type (WT), and carrying H3K27me3 on gene bodies in mouse ESCs (n = 3457) were subdivided into genes that show up-regulated (red, n = 1067), down-regulated (blue, n = 93) and unchanged (gray, n = 2297) levels of mRNA in EedKO compared with WT ESCs (Supplementary Note, Methods). (right) Violin plots showing log2 fold changes of transcription end site (TES) RNAPII-S2P levels in EedKO mutant compared with WT ESCs. g, Chromatin profiles of Fos in WT and EedKO ESCs. While stalled RNAPII-S5P showed decrease in the promoter (pink highlight), elongating RNAPII-S2P was increased (green highlight) in EedKO ESCs. h, MA-plots comparing mRNA levels of bipartite (Bip) genes (n = 100, red) between full Ezh1KO;Ezh2KO (left) or Ezh2 catalytically inactive Ezh1KO;Ezh2Y726D (right) with WT ESCs. d and f, Plots extend from the data minima to the maxima with the white dot or middle bar indicating median, the box showing the interquartile range and whiskers extending to the most extreme data point within 1.5X the interquartile range. P value is from a two-sided Wilcoxon’s test between the two groups.
Extended Data Fig. 8 IEG bipartite chromatin is necessary to prevent precocious activity-dependent neuronal maturation.
a, Short time (two days) E12.5 ex vivo-cultured Drg11tdTomato/+ hindbrains. After over-night (o/n) treatment with a cocktail of neuronal activity blockers (TDN cocktail = TTX + D-AP5 + NBQX, inhibitors of sodium channel, NMDAR and AMPAR), cultured neurons were treated by 55 mM KCl for 1 hour. Drg11-positive immature trigeminal neurons were FACS-isolated for ATAC-seq analysis. Violin plots visualize log2 fold changes of enhancer chromatin accessibilities in 1 hour KCl-treated neurons as compared to non-treated control neurons. Increased accessibility is selectively detected in KCl-treated neurons at activity-dependent Fos-binding enhancers that normally become open only at P4 (green, n = 85 enhancers) (purple, all non-Fos-binding enhancers that gain accessibilities only at P4, n = 3882 enhancers). Plots extend from the data minima to the maxima with the white dot indicating median, the box showing the interquartile range and whiskers extending to the most extreme data point within 1.5X the interquartile range from the box. P value is from a two-sided Wilcoxon’s test. b, Scatterplots comparing enhancer accessibilities (ATAC) in E14.5 Ezh2 heterozygous control (ctrl) and homozygous mutant (Ezh2cKOHB-RFP) hindbrain cells. All the barrelette enhancers in Drg11vPrV-ZsGreen/+ barrelette neurons (left), non-Fos-binding enhancers that gain accessibilities at P4 as compared with E14.5 in Drg11vPrV-ZsGreen/+ barrelette neurons (n = 3882 enhancers, middle, purple), neuronal activity-dependent Fos-binding enhancers that gain accessibilities at P4 as compared with E14.5 Drg11vPrV-ZsGreen/+ barrelette neurons (n = 85 enhancers, left, green) are shown (Methods). 85 activity-dependent Fos-binding enhancers show precocious opening upon H3K27me3 removal at E14.5. Also see Fig. 5d.
a, H3K27me3 profiles of the Fos locus in E14.5 Drg11vPrV-ZsGreen/+ barrelette neurons and E12.5 cultured hindbrain neurons at day 1 and day 7 of culture. One week hindbrain neuron culture results in the loss of the H3K27me3 mark from the Fos gene body, similarly to one-week embryonic cortical neuron culture (Extended Data Fig. 2a); in contrast, short-term (day 1) cultured hindbrain neurons still maintain H3K27me3 levels comparable to E14.5 barrelette neurons. b, H3K27me3 levels at the Fos locus in short-term cultured E12.5 hindbrain neurons overexpressing control dCas9 (green) or dCas9-UTX (red) targeted to Fos gene body: three biological replicates overlaid. Genomic regions targeted by guide-RNAs (gRNAs) are indicated. c, Averaged H3K27me3 profiles of Fos (left) and the rest of the E14.5Bip genes (right). Overexpression of control dCas9 (green) or dCas9-UTX (red) are compared. d, (left) MA-plot comparing H3K27me3 levels of dCas9-UTX against dCas9 targeting to Fos locus. Fos (red dot) shows a loss of gene body H3K27me3 compared to control genes carrying similar levels of H3K27me3 (green dots). (right) Density plot (green line) shows the distribution of the logFC values of the selected control genes (greed dots), highlighting the Fos logFC (red line) in the 1.48 % lower tail of the density plot and logFC of E14.5Bip genes (yellow line), indicating slight but significant decrease in Fos H3K27me3. n = 3 biologically independent neuron cultures. e, mRNA levels of Actb, Gapdh and Fos determined by RT-qPCR in short-term cultured E12.5 hindbrain neurons overexpressing control dCas9 (green) or dCas9-UTX (purple) targeted to Actb (left) or Gapdh (right) loci (n = 6 biologically independent neuron cultures). The median expression is indicated by bars. P values are from Welch’s two-sample two-sided t-tests. NS: not significant (P > 0.05).
Extended Data Fig. 10 Polycomb marking of bipartite gene bodies regulates the rapidity and amplitude of transcriptional response to relevant stimuli.
a, Genome browser view of bivalent Junb in E14.5 Drg11vPrV-ZsGreen/+ barrelette neurons. Chromatin accessibility (ATAC), H3K4me2, H3K27ac and H3K27me3 are shown. b, mRNA levels of bipartite (Fos, Egr1) and bivalent (Junb) ARGs, determined by RT-qPCR in E14.5 hindbrain cells treated by KCl for 8 (left) or 30 min (right) (n = 4, biologically independent embryos). The median expression is indicated by bars. P values are from Welch’s two-sample two-sided t-tests. NS: not significant (p > 0.05). c, mRNA levels of Fos (left) and Egr1 (right), determined by RT-qPCR in serum-starved WT (green) and EedKO (purple) mouse ESCs (n = 4, biologically independent cultured cells) treated with a low (1%) or high (10%) concentration of Fetal Calf Serum (FCS) for 16 minutes. WT ESCs Fos and Egr1 could be induced only after prolonged exposure (that is 16 minutes) to 1% FCS: also see the effects of shorter (that is 8 minutes) time exposure to 1% FCS in Fig. 5f and g. The median expression is indicated by bars. P values are from Welch’s two-sample two-sided t-tests.
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Kitazawa, T., Machlab, D., Joshi, O. et al. A unique bipartite Polycomb signature regulates stimulus-response transcription during development. Nat Genet 53, 379–391 (2021). https://doi.org/10.1038/s41588-021-00789-z
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