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Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos

Nature Genetics volume 53, pages 551–563 (2021)Cite this article

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An Author Correction to this article was published on 22 April 2021

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Abstract

Polycomb repressive complexes 1 and 2 (PRC1/2) maintain transcriptional silencing of developmental genes largely by catalyzing the formation of mono-ubiquitinated histone H2A at lysine 119 (H2AK119ub1) and trimethylated histone H3 at lysine 27 (H3K27me3), respectively. How Polycomb domains are reprogrammed during mammalian preimplantation development remains largely unclear. Here we show that, although H2AK119ub1 and H3K27me3 are highly colocalized in gametes, they undergo differential reprogramming dynamics following fertilization. H3K27me3 maintains thousands of maternally biased domains until the blastocyst stage, whereas maternally biased H2AK119ub1 distribution in zygotes is largely equalized at the two-cell stage. Notably, while maternal PRC2 depletion has a limited effect on global H2AK119ub1 in early embryos, it disrupts allelic H2AK119ub1 at H3K27me3 imprinting loci including Xist. By contrast, acute H2AK119ub1 depletion in zygotes does not affect H3K27me3 imprinting maintenance, at least by the four-cell stage. Importantly, loss of H2AK119ub1, but not H3K27me3, causes premature activation of developmental genes during zygotic genome activation (ZGA) and subsequent embryonic arrest. Thus, our study reveals distinct dynamics and functions of H3K27me3 and H2AK119ub1 in mouse preimplantation embryos.

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Fig. 1: H2AK119ub1 (H2Aub) in mouse oocytes and early embryos is highly dynamic.
Fig. 2: Loss of parental H2Aub asymmetric distribution during preimplantation development.
Fig. 3: Distinct dynamics of H2Aub and H3K27me3 during preimplantation development.
Fig. 4: Loss of maternal Eed has a limited effect on global H2Aub except for maternal H3K27me3-dependent imprinted genes.
Fig. 5: Acute depletion of H2Aub in zygotes has minimal immediate effects on H3K27me3.
Fig. 6: Acute depletion of H2Aub causes premature activation of developmental genes during ZGA and leads to early embryonic arrest.
Fig. 7: Models of the allelic dynamics of H2Aub and H3K27me3.

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Data availability

All sequencing data were deposited in the Gene Expression Omnibus under accession number GSE153531.

Code availability

The code for this study is available at https://github.com/YiZhang-lab/H2Aub_K27me3_preimplantation_dynamics.

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Acknowledgements

We thank C. Zhang and W. Zhang for critical reading of the manuscript. This project was supported by the NIH (R01HD092465) and the HHMI. Y.Z. is an Investigator of the Howard Hughes Medical Institute.

Author information

Author notes

  1. Mohamed Nadhir Djekidel

    Present address: Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA

  2. These authors contributed equally: Zhiyuan Chen, Mohamed Nadhir Djekidel.

Authors and Affiliations

  1. Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA

    Zhiyuan Chen, Mohamed Nadhir Djekidel & Yi Zhang

  2. Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA, USA

    Zhiyuan Chen, Mohamed Nadhir Djekidel & Yi Zhang

  3. Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA

    Zhiyuan Chen, Mohamed Nadhir Djekidel & Yi Zhang

  4. Department of Genetics, Harvard Medical School, Boston, MA, USA

    Yi Zhang

  5. Harvard Stem Cell Institute, WAB-149G, Boston, MA, USA

    Yi Zhang

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  1. Zhiyuan Chen
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Contributions

Y.Z. conceived the project. Z.C. and Y.Z. designed the experiments. Z.C. performed the experiments. M.N.D. performed most of the bioinformatic analyses, and Z.C. analyzed some of the ChIP-seq, CUT&RUN and RNA-seq datasets. All authors were involved in the interpretation of data. Z.C. and Y.Z. wrote the manuscript with M.N.D.’s input.

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Correspondence to Yi Zhang.

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Extended data

Extended Data Fig. 1 H2Aub dynamics in oocytes and early embryos.

a, Genome browser view of H2Aub profiles in oocytes and early embryos. The H2Aub ChIP-seq data of mESC were obtained from24. b, Bar plots showing the reproducibility of the biological replicates of H2Aub CUT&RUN datasets. The H2Aub enrichment was calculated as reads per kilobase per million reads (RPKM) by 5-kb bin. The Pearson correlation co-efficient are also shown. c, Heatmap with hierarchical clustering showing the correlation of global H2Aub enrichment between oocytes and early embryos. d, Bar plot showing the percentage of genomic regions occupied by H2Aub domains (regions with H2Aub signal determined using ChromHMM) at different developmental stages. e, Bar plot showing the percentage of H2Aub CUT&RUN reads that are mapped to each ChromHMM type at different developmental stages.

Extended Data Fig. 2 Allelic dynamics of H2Aub in preimplantation development.

a, Genome browser views comparing our sperm H3K27me3 STAR ChIP-seq data with publicly available datasets22,55 b, Venn diagram showing that most H3K27me3 domains identified are common between Zheng et al., and our data. c, Genome browser view showing sperm H2Aub STAR ChIP-seq. d, Scatter plot showing the reproducibility of the biological replicates of H2Aub sperm ChIP-seq datasets. The H2Aub enrichment was calculated as reads per kilobase per million reads (RPKM) by 5-kb bin. The Pearson correlation co-efficient is also shown. e, Bar plot showing the number of allelically biased H2Aub regions at different developmental stages. Maternally (Mat) and paternally (Pat) biased H2Aub regions were identified by merging adjacent allelically biased 5kb bins meeting cutoff: fold change (FC) > 2 and adjusted p-value (p-adj) < 0.01. P values were calculated using a binomial exact test of the null hypothesis that both alleles are equally enriched and adjusted using Benjamin & Hochberg method. f, Box plot showing the expression levels of genes within allelically biased H2Aub regions at 1-cell stage. The number of genes within maternally or paternally biased H2Aub domains at 1-cell were 1113 and 15, respectively. The middle lines in the boxes represent medians. Box hinges indicate the twenty-fifth and seventy-fifth percentiles, the whiskers indicate the hinge ± 1.5 × interquartile range, and the dots represent outliers. RNA-seq data were obtained from47. Mat: maternal allele; Pat: paternal allele. g, Heatmaps showing allelic dynamics of the H2Aub regions that are not allelically biased at 1-cell during preimplantation development. The number of regions for each category are indicated. h, Genome browser view of allelic dynamics of the H2Aub regions that are not allelically biased at 1-cell during preimplantation development.

Extended Data Fig. 3 Distinct non-allelic dynamics of H3K27me3 and H2Aub in preimplantation embryos.

a, Genome browser view of H3K27me3, H2Aub and H3K36me348 dynamics in oocytes and preimplantation embryos. b, Venn diagrams showing overlaps of H3K27me3 and H2Aub domains at different developmental stages. The H3K27me3 ChIP-seq data in panels A and B were from17,22. c, Heatmap showing enrichment of H3K27me3, H2Aub, and H3K36me3 at H2Aub domains identified in GV oocytes. The GV H2Aub domains were classified into six groups based on dynamics of these histone modifications during development.

Extended Data Fig. 4 Distinct allelic dynamics of H3K27me3 and H2Aub in preimplantation embryos.

a, Genome browser view of allelic H3K27me3 and H2Aub dynamics at the indicated embryonic stages. Note that maternally biased H2Aub at 1-cell becomes equalized at 2-cell stage by gaining H2Aub on the paternal allele. However, H3K27me3 maintains maternally biased from 1-cell to morula stage. The H3K27me3 ChIP-seq/CUT&RUN data were from22,33. M: maternal; P: paternal. b, Genome browser view of allelic H3K27me3 and H2Aub at Jade1 (also known as Phf17) and Sfmbt2 locus. Note that maternal-biased H2Aub is lost at the imprinted loci in 2-cell embryos then regain during later development. In contrast, maternal biased H3K27me3 is maintained from 1-cell to morula stage. c, Box plots showing allelic bias of H2Aub at gene bodies of the 76 putative maternal H3K27me3-dependent imprinted genes. The left panel represents genes showing transient loss and regain of H2Aub allelic bias in early development, whereas the right panel shows genes that loss of H2Aub allelic bias after 2-cell stage. The middle lines in the boxes represent medians. Box hinges indicate the twenty-fifth and seventy-fifth percentiles, the whiskers indicate the hinge ± 1.5 × interquartile range, and the dots show outliers. Mat: maternal; Pat: paternal.

Extended Data Fig. 5 Loss of maternal Eed has limited effect on global H2Aub except the maternal H3K27me3-dependent imprinted loci.

a, Relative intensity of the H3K27me3 and H2Aub signal in 1-cell, 2-cell, and 4-cell embryos. For 1-cell embryos, only signals on the maternal pronuclei were measured. The average signal intensity of CTR embryos was set as 1.0. The total number of embryos analyzed were 9 (CTR) and 7 (matKO) for 1-cell embryos, 6 (CTR) and 6 (matKO) for 2-cell embryos, and 7 (CTR) and 8 (matKO) for 4-cell embryos, respectively. Center dot and error bars indicate mean and standard deviation, respectively. matKO: maternal knockout. b, Scatter plots showing the reproducibility between biological replicates of H2Aub CUT&RUN datasets. The H2Aub enrichment was calculated as RPKM in 5-kb bins. The Pearson correlation co-efficient are also shown. CKO: conditional knockout. c, Hierarchical clustering of maternal (M) and paternal (P) alleles of preimplantation embryo and GV oocytes based on their global H2Aub enrichment. d, Genome browser view showing comparable enrichment of H2Aub between CTR and CKO in GV oocytes and between CTR and matKO in preimplantation embryos. e, Genome browser view showing H2Aub enrichment at Gab1 and Sfmbt2 loci in CTR and Eed CKO GV oocytes and matKO morula embryos.

Extended Data Fig. 6 Quality control of acute H2Aub depletion and CUT&RUN datasets.

a, Representative zygotes immunostaining images. M: maternal pronucleus; P: paternal pronucleus; h: human; CTR: control; OE: over-expression; PR-DUB: Polycomb repressive deubiquitinase; WT: wild type. scale bar: 20 µm. The quantifications are in panel B) Relative H2Aub signal intensity of zygotes. Only signal on the maternal pronuclei (matPN) was measured. The number of embryos analyzed were 6 for non-injected, 11 for hBAP1 (C91A), 20 for CTR, 10 for hBAP1 (WT), and 22 for OE, respectively. c, Relative H2Aub signal intensity of 2-cell and 4-cell embryos. The number of embryos analyzed were 2 for non-injected 2-cell, 3 for CTR 2-cell, 3 for OE 2-cell, 9 for non-injected 4-cell, 10 for CTR 4-cell, and 9 for OE 4-cell, respectively. For Panel B-C), center dot and error bars indicate mean and standard deviation, respectively. d, Scatter plot comparing H2Aub enrichment between non-injected and CTR 4-cell embryos. Pearson correlation co-efficient is shown. e, Stacked bar plot showing the overlap between the top 1000 bins and RING1B-binding sites identified in mESCs24. f, Box plots showing RING1B signals in mESCs and the H2Aub levels in CTR and OE embryos at rank ordered RING1B-binding sites (n = 8833). The bottom 5 (Bot5%, n = 442), top 5 (Top5%, n = 442), and middle 50 percentile (Mid50%, n = 4416) RING1B sites are indicated. The middle lines in the boxes represent medians. Box hinges indicate the twenty-fifth and seventy-fifth percentiles, the whiskers indicate the hinge ± 1.5 × interquartile range. P-value was calculated by Wilcoxon test (two-sided). g, Bar plots showing reproducibility of the biological replicates of H3K27me3 CUT&RUN datasets. The Pearson correlation co-efficient are shown. h, Genome browser view of H2Aub and H3K27me3 enrichment at the Jade1 and Sfmbt2 loci in 4-cell embryos.

Extended Data Fig. 7 The transcriptional effects of H2Aub and H3K27me3 depletion in early embryos.

a, Heatmap showing the correlation between replicates of PR-DUB RNA-seq samples. b, Left panel shows representative immunostaining images of zygotes. M: maternal pronucleus; P: paternal pronucleus; Pb: polar body. scale bar: 20 µm. Right panel shows quantification of the H3K27me3 signal intensity. Only signal on the maternal pronuclei (matPN) was measured. The number of embryos analyzed were 8 for non-injected, 4 for KDM6b (CTR), and 8 for KDM6b (OE), respectively. Center dot and error bars indicate mean and standard deviation, respectively. C) Heatmap showing the correlation between replicates of Kdm6b and Eed RNA-seq samples. d, Scatter plot comparing gene expression levels of KDM6B (CTR) and (OE) 2-cell and 4-cell embryos. fold change (FC) >2, P-value < 0.05, FPKM > 1. e, Scatter plot comparing gene expression levels of Eed (CTR) and (matKO) 2-cell embryos. fold change (FC) >2, P-value < 0.05, FPKM > 1. f, Left panel, heatmaps of the genes up-regulated by H2Aub removal in 2-cell embryos; Right panel, heatmaps showing expression dynamics of the genes on the left panel at different developmental stages. RNA-seq data in right panel were from17,20,74,75. G) Box plots comparing the expression levels of ZGA and maternal decay genes. The middle lines in the boxes represent medians. Box hinges indicate the twenty-fifth and seventy-fifth percentiles, the whiskers indicate the hinge ± 1.5 × interquartile range. The ZGA (n = 3090) and maternal decay (n = 2343) genes were identified by comparing 2-cell and MII oocytes total RNA-seq data (Supplementary Table 1). Genes up- and down- regulated in 2-cell versus MII oocyte were defined as ZGA and maternal decay genes, respectively. fold change > 5, p-value < 0.05, and RPKM > 1.

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Chen, Z., Djekidel, M.N. & Zhang, Y. Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos. Nat Genet 53, 551–563 (2021). https://doi.org/10.1038/s41588-021-00821-2

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