Abstract

The oocyte epigenome plays critical roles in mammalian gametogenesis and embryogenesis. Yet, how it is established remains elusive. Here, we report that histone-lysine N-methyltransferase SETD2, an H3K36me3 methyltransferase, is a crucial regulator of the mouse oocyte epigenome. Deficiency in Setd2 leads to extensive alterations of the oocyte epigenome, including the loss of H3K36me3, failure in establishing the correct DNA methylome, invasion of H3K4me3 and H3K27me3 into former H3K36me3 territories and aberrant acquisition of H3K4me3 at imprinting control regions instead of DNA methylation. Importantly, maternal depletion of SETD2 results in oocyte maturation defects and subsequent one-cell arrest after fertilization. The preimplantation arrest is mainly due to a maternal cytosolic defect, since it can be largely rescued by normal oocyte cytosol. However, chromatin defects, including aberrant imprinting, persist in these embryos, leading to embryonic lethality after implantation. Thus, these data identify SETD2 as a crucial player in establishing the maternal epigenome that in turn controls embryonic development.

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Data availability

The generated and analyzed datasets in the current study are available in the Gene Expression Omnibus with accession number GSE112835.

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Acknowledgements

We thank members of the Xie laboratory for their comments during the preparation of the manuscript. We thank F. Gao for providing the Gdf9-Cre mice. We are thankful for the support provided by the animal core, sequencing core and biocomputing facilities at Tsinghua University. This work was funded by the National Natural Science Foundation of China (grant nos. 31422031 and 31725018 to W.Xie; grant no. 81772938 to L.Li), National Key R&D Program of China (grant no. 2016YFC0900300 to W.Xie), the National Basic Research Program of China (grant no. 2015CB856201 to W.Xie), Beijing Municipal Science & Technology Commission (grant no. Z181100001318006 to W.Xie), Science and Technology Commission of Shanghai Municipality (grant nos. 16140902100 and 18140902700 to L.Li), the THU-PKU Center for Life Sciences (W.Xie), by the Canadian Institutes of Health Research (grant no. MOP-133417 to M.C.L. and grant no. MOP-119357 to L.Lefebvre) and by National Cancer Institute, National Institutes of Health (grant no. CA231993 and CA203012 to C.L.W.). Q.X. is supported by postdoctoral fellowships from the Tsinghua-Peking Joint Center for Life Sciences. L.Li is supported by an Innovation Research Plan from the Shanghai Municipal Education Commission (grant no. ZXGF082101) and funds from State Key Laboratory of Oncogenes and Related Genes (grant no. KF01801). W.Xie is a recipient of an HHMI International Research Scholar award.

Author information

Author notes

  1. These authors contributed equally: Qianhua Xu, Yunlong Xiang, Qiujun Wang, Leyun Wang.

Affiliations

  1. Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China

    • Qianhua Xu
    • , Yunlong Xiang
    • , Qiujun Wang
    • , Yu Zhang
    • , Bingjie Zhang
    • , Guang Yu
    • , Weikun Xia
    • , Zhenhai Du
    • , Chunyi Huang
    • , Jing Ma
    • , Hui Zheng
    • , Yuanyuan Li
    •  & Wei Xie
  2. State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China

    • Leyun Wang
    • , Chao Liu
    •  & Wei Li
  3. Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada

    • Julie Brind’Amour
    • , Aaron Blair Bogutz
    • , Louis Lefebvre
    •  & Matthew C. Lorincz
  4. Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA

    • Cheryl Lyn Walker
  5. Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    • Eric Jonasch
  6. Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Wuhan University, Wuhan, China

    • Min Wu
  7. State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China

    • Li Li

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Contributions

Q.X., Y.X. and W.Xie conceived and designed the project. Q.X. and Y.X. performed the STAR ChIP-seq library construction. Y.X. and Q.W. performed the RNA-seq library construction. Y.Z. performed the STEM-seq experiment. Y.X. analyzed the STAR ChIP-seq and RNA-seq data. Y.X. and Q.W. analyzed the methylome data. Q.X. and Y.X. collected the oocytes and embryos. L.Li and M.W. generated and provided the Setd2loxP/loxP mice. Q.X., Y.X. and Q.W. maintained and genotyped the mice. Z.D. performed mature sperm sorting and B.Z. performed the sperm ChIP-seq. C.H. and J.M. maintained and prepared the PWK/PhJ mice for ICSI. B.Z. and H.Z. provided technical support for the STAR ChIP-seq and data analysis. L.W. and C.L. performed the spindle transfer, ICSI and embryonic culture under the supervision of W.L. G.Y. and W.Xia assisted with chromatin analysis of reconstructed embryos. Q.X. performed the mouse embryo experiments and immunostaining. Q.W. and Y.L. performed the NGS sequencing. C.L.W. and E.J. provided Setd2loxPf/loxP mice, and A.B.B., J.B.A. and L.Lefebvre performed Setd2loxPf/loxP;Zp3-Cre related experiments. M.C.L., W.L., L.Li and W.Xie supervised the project or related experiments. Q.X., Y.X. and W.Xie prepared the manuscript and figures with the help from all authors.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Wei Li or Li Li or Wei Xie.

Integrated supplementary information

  1. Supplementary Fig. 1 Characterization of H3K36me3 during mouse oogenesis.

    a, Scatter plots showing whole genome H3K36me3 enrichment (10kb window) between 500 cells (n = 1), 10k cells (n = 1) and ENCODE dataset in mESCs. Pearson correlation is also shown. b, Pearson correlations are shown for pairwise comparisons of H3K36me3 enrichment between individual sample. Analyses were done using two replicates for GO-P7, GO-P10, GO-P14, FGO, and MII oocytes, and one replicate for 500 and 10k mESCs. ENCODE H3K36me3 data of mESCs is used for comparison. c, Hierarchical clustering analysis of H3K36me3 in individual replicates of mouse early embryos at various stages or mESCs with various cell numbers. d, The dynamics of gene expression and histone modifications for genes activated between GO-P7 to GO-P14.

  2. Supplementary Fig. 2 Characterization of Dnmt3L−/− and Setd2mNull FGOs.

    a, Strategy of depleting exon 4-7 in the ADD (ATRX-DNMT3-DNMT3L) domain of Dnmt3L (Methods). Inner and outer primers are designed for genotyping. b, Spleen from control and Dnmt3L/ mice was isolated and western blotting was performed. The asterisk marks possible non-specific band. The arrow marks DNMT3L band. Blot image was cropped (see Supplementary Fig. 13). The experiments were independently performed three times. c, Agarose gel shows the genotyping result of control and Dnmt3L/ mice by extracting genomic DNA from mouse tail and performing PCR amplification. For mutant mice, the product of inner primer cannot be detected and the outer primer product is truncated. Similar results were obtained from three independent experiments. d, Violin plot showing the levels of DNA methylation in control (n = 2) and Dnmt3L/ (n = 2) oocytes in FGO. The outer shape indicates all results. The center dot indicates the median average value, and the thick and thin line represent 50% and 95% value ranges, respectively. e, Scatter plot showing gene expression in Dnmt3L+/ and Dnmt3L/ FGO. Pearson correlation coefficient is shown. Differentially expressed genes are also shown in red (up-regulated) and blue (down-regulated) (2-fold change).

  3. Supplementary Fig. 3 Aberrant DNA methylation in Setd2mNull FGOs.

    a, H3K36me3 staining in control (n = 20) and Setd2mNull FGO (n = 20). A representative image from 3 independent experiments is shown. Scale bars: 20 μm. Quantification of H3K36me3 intensity normalized against DNA staining by Hoechst is also shown. Each dot represents the IF intensity of H3K36me3 in nucleus, with mean value indicated by horizontal lines. Error bar represents s.e.m. P-value (t-test with Welch correlation, two sided) is shown. b, Average plot showing H3K36me3 enrichment at gene body of control (n = 2) and Setd2mNull FGO (n = 2). c-d, EU straining in NSN and SN oocytes in control and Setd2mNull FGO. Diagram showing ratios between NSN and SN in control (n = 52) and Setd2mNull FGO (n = 62) (radius between 70-80 μm). e, α-Tubulin staining in control and Setd2mNull MII oocytes. Arrow shows a polar chromosome. Scale bars: 20 μm. These experiments were performed independently three times. f, Gene expression levels (FPKM) of Dnmts in control (n = 2) and Setd2mNull (n = 2) FGO. Centre line indicates average FPKM value between replicates. Error bar represents s.e.m. g, Averaged 5mC enrichment patterns for chromosome 12 in control and Setd2mNull FGO. Gene desert regions with DNA methylation changes are shaded. h, The numbers of 1-kb bins that gain, lose, or show no changes of DNA methylation in Setd2mNull FGOs. i, Percentages of 1-kb bins that gain, lose, or show no changes of DNA methylation in Setd2mNull FGOs that fall into compartment A/B, respectively. Percentages of whole genome in compartment A/B is shown as a control.

  4. Supplementary Fig. 4 Aberrant H3K4me3 and H3K27me3 in Setd2mNull FGOs.

    a, Pie charts demonstrating proportions of the genome covered by H3K4me3, H3K27me3, bivalent marks (H3K4me3 and H3K27me3), H3K36me3, or none of these marks in control and Setd2mNull FGO (Methods). b, A snapshot of UCSC browser showing H3K4me3, H3K27me3 and H3K36me3 enrichment in 2-3 replicates of control and Setd2mNull FGO. Regions that acquire/lost H3K4me3 or acquire H3K27me3 are shaded. c, Box plots showing enrichment of H3K4me3 and H3K27me3 for regions defined as ‘K4me3-gain domains’, ‘K4me3-loss domains’, ‘K27me3-gain domains’, and ‘K27me3-loss domains’ in individual replicates of control (H3K4me3, n = 3; H3K27me3, n = 2) and Setd2mNull FGO (H3K4me3, n = 3; H3K27me3, n = 2). The median of each dataset is shown by center line. The bottom, top edges and whiskers represent the 25th, 75th percentiles and 1.5 times the interquartile range, respectively. d, Box plots showing enrichment of H3K4me3 and H3K27me3 in control (H3K4me3, n = 3; H3K27me3, n = 2) and Setd2mNull FGO (H3K4me3, n = 3; H3K27me3, n = 2) for regions defined as ‘K4me3-gain domains’, ‘K4me3-loss domains’, ‘K27me3-gain domains’, and ‘K27me3-loss domains’. Enrichment of whole genome is shown as controls. The median of each dataset is shown by center line. The bottom, top edges and whiskers represent the 25th, 75th percentiles and 1.5 times the interquartile range, respectively. P-values (t-test, two sided) are also shown.

  5. Supplementary Fig. 5 Setd2mNull GO-P7 oocytes share a similar epigenome with Setd2mNull FGOs.

    a, Snapshots from UCSC genome browser showing H3K4me3 and H3K27me3 enrichment in control and Setd2mNull GO-P7 and FGO oocytes. b, Box plots showing enrichment of H3K4me3 and H3K27me3 in control (Zhang et al., 2016) and Setd2mNull P7 oocytes (H3K4me3, n = 1; H3K27me3, n = 1) for regions defined as ‘K4me3-gain domains’, ‘K4me3-loss domains’, ‘K27me3-gain domains’, and ‘K27me3-loss domains’ in control and Setd2mNull FGO. Similar analysis was performed for transcription levels in control (n = 2) and Setd2mNull P7 oocytes (n = 2) for misregulated (up, upregulated; down, downregulated) genes in Setd2mNull FGO. The median of each dataset is shown by center line. The bottom, the top edges and whiskers represent the 25th, 75th percentiles and 1.5 times the interquartile range, respectively. P-values (t-test, two sided) are also shown. c, Hierarchical clustering analysis of global H3K4me3 and H3K27me3 distribution in control (Zhang et al., 2016) and Setd2mNull GO-P7 and FGO. d, Violin plot showing the levels of DNA methylation in control (GO-P7, n = 1; FGO, n = 2) and Setd2mNull oocytes (GO-P7, n = 1; FGO, n = 2) in GO-P7 and FGO. The outer shape indicates all results. The center dot indicates the median average value, and the thick and thin line represent the 50% and 95% value ranges, respectively.

  6. Supplementary Fig. 6 Ectopic H3K27me3 correlates with the downregulation of gene expression in Setd2mNull FGOs.

    a, Heat maps showing differentially expressed genes (2-fold change) that also show altered H3K4me3 in gene bodies in Setd2mNull FGO. Promoter H3K4me3 levels are also mapped and shown. Genes showing changes in both gene expression and H3K4me3 were selected for this analysis. b, Heat maps showing differentially expressed genes (2-fold change) that also show alteration of H3K27me3 enrichment at gene bodies in Setd2mNull FGO. Promoter H3K27me3 levels are also mapped and shown. Genes showing changes in both gene expression and H3K27me3 were selected for this analysis. Gene ontology analysis and example genes are also shown on the right side. c, Scatter plot showing changes of gene expression and changes of H3K4me3 (n = 3) or H3K27me3 (n = 2) at promoters in Setd2mNull FGO, compared to control FGO (n = 2 for both H3K4me3 and H3K27me3). Pearson correlation coefficient is shown. d, A snapshot from UCSC browser showing H3K4me3, H3K27me3 and H3K36me3 enrichment in control and Setd2mNull FGO. Gene expression is also shown.

  7. Supplementary Fig. 7 Abnormal imprints in Setd2mNull FGOs.

    a, Snapshots from UCSC browser showing H3K4me3, H3K27me3, H3K36me3, and DNA methylation levels at maternal imprinted loci in control and Setd2mNull FGO, as well as WT and Dnmt3a/b-/- oocytes. Imprinting control regions are shaded. b, Box plot showing the DNA methylation level in regions with H3K4me3, H3K27me3, or neither in Setd2mNull FGO (n = 2). The median of each dataset is shown by center line. The bottom, top edges and whiskers represent the 25th, 75th percentiles and 1.5 times the interquartile range, respectively. P-values (t-test, two sided) are also shown.

  8. Supplementary Fig. 8 Dynamics of H3K36me3 in mouse early embryos.

    a, Immunostaining of H3K36me3 in oocytes and early embryos. Scale bars: 20 μm. One representative result out of three independent experiments is shown. PB, polar body. b, A snapshot of UCSC browser showing H3K36me3 enrichment in two replicates of sperm, 1C, late 2C, 8C and ICM from blastocyst. c, Hierarchical clustering analysis of H3K36me3 in individual replicates of mouse early embryos at various stages. d, Pearson correlations for pairwise comparisons of H3K36me3 enrichment at individual stages (n = 2). Two replicates were done for each sample. e, A bar chart showing the percentages of reads assigned to the maternal or paternal allele in mouse embryos at individual stage.

  9. Supplementary Fig. 9 Allelic H3K36me3 in early embryos.

    a, Hierarchical clustering analysis of H3K36me3 at individual stage of mouse early embryos. b, Heat maps showing allelic H3K36me3 enrichment and related allelic gene expression in mouse early embryos. c, Snapshots showing allelic H3K36me3 and H3K27me3 at Sfmbt2, Eva1a, Adam19 and Bzw2 loci.

  10. Supplementary Fig. 10

    a, Bright fields of mouse embryos isolated at E2.5 for control (morula stage) and Setd2mNull embryos (arrested at 1-cell stage). One representative result of three independent experiments is shown. Scale bars: 20 μm. b, Hoechest staining of control (2-cell) and Setd2mNull embryos (arrested at 1-cell prior to pronuclei fusion) obtained at E1.5. One representative result of two independent experiments is shown. Scale bars: 20 μm. c, Bright fields of mouse embryos isolated at E3.5 for control (blastocyst stage) and Setd2f/f;Zp3-Cre embryos. One representative result of two independent experiments is shown. Scale bars: 20 μm. d, EU staining in control and Setd2mNull zygotes at E0.5 (1-cell stage). Dashed lines marked maternal and paternal pronuclei. One representative result of three independent experiments is shown. e, EU signal intensity was calculated by immunofluorescence intensity of maternal/paternal pronuclei against background in control (n = 9) and Setd2mNull zygotes (n = 10) . IF intensity of individual pronuclei from three independent experiments are analyzed. Dots represent single pronuclei, with medians indicated by horizontal lines. Error bar represents s.e.m.. f, Hierarchical clustering analysis of global gene expression in oocytes and early embryos for control (blue) and Setd2mNull mutants (red). g, Heat map showing gene expression in control and Setd2mNull oocytes and embryos.

  11. Supplementary Fig. 11 Aberrant epigenome in Setd2mNull 1-cell embryos.

    a, Gene ontology of up- or down-regulated genes between Setd2mNull (n = 2) and control 1C (n = 2). P-values (t-test, two sided, not adjusted by multiple comparisons) are transformed by log10. b, Gene ontology of genes that are both up- or down-regulated between Setd2mNull and control in FGO (n = 2) and 1C embryos (n = 2). P-values (t-test, two sided, not adjusted by multiple comparisons) are transformed by log10. c, Heat map showing expression and H3K27me3 levels for genes that are both downregulated in Setd2mNull FGO and 1C embryos, and acquire ectopic H3K27me3 in Setd2mNull FGO or 1C embryos. Example genes are also shown. d, A heat map showing H3K4me3 enrichment in FGO and 1C for ‘H3K4me3-gain domains’ or ‘H3K4me3-loss domains’ defined in FGO (left). A similar analysis result was shown for H3K27me3 (right). e, Snapshots from UCSC genome browser showing allelic H3K4me3 (top) or H3K27me3 (bottom) enrichment in control and Setd2mNull zygotes. H3K4me3 and H3K27me3 in 1C embryos from a previous study are also shown as control. f, A bar chart showing the percentages of H3K4me3 or H3K27me3 reads assigned to the maternal (129 or C57BL/6) or paternal (PWK) allele in control and Setd2mNull 1C embryos.

  12. Supplementary Fig. 12 Development of reconstructed embryos.

    a, Reconstructed embryos (Cwt+Mwt+Pwt, n = 78; Cwt+Mmut+Pwt, n = 74; Cmut+Mwt+Pwt, n = 22) were cultured to 24h, 48h and 96h after spindle transfer, respectively. One representative result of five independent experiments is shown. Scale bars: 20 μm. b, Morphology of Cwt+Mwt+Pwt (n = 44) and Cwt+Mmut+Pwt (n = 38) embryos dissected from E10.5. One representative image from 2-3 independent experiments is shown. Pl, placenta; Em, embryo; YS, yolk sac; EPC, ectoplacental cone. c, Box plots showing enrichment of H3K4me3 and H3K27me3 for regions defined as ‘K4me3-gain/loss domains’, ‘K27me3-gain/loss domains’, in control and Cwt+Mmut+Pwt embryos at early 2C (H3K4me3, n = 1; H3K27me3 n = 1) and 8C (H3K4me3, n = 1; H3K27me3 n = 1). The median of each dataset is shown by center line. The bottom, top edges and whiskers represent the 25th, 75th percentiles and 1.5 times the interquartile range, respectively. P-values (t-test, two sided) are shown. d, Snapshot from UCSC browser showing H3K4me3 enrichment at a maternally imprinted locus in control, Setd2mNull FGO, ST embryos, with gene expression at 8C. e, A model illustrating epigenetic reprogramming in control and mutant FGOs or embryos. In Setd2mNull FGO, H3K27me3 and H3K4me3 ectopically spread to former H3K36me3 territories (Gene1 and Gene2). The aberrant epigenome persists to early 2-cell embryos even in reconstructed embryos with WT cytosol (Cwt+Mmut+Pwt). At 8-cell stage, the aberrant H3K4me3 is largely globally reset to canonical H3K4me3, except for ectopic H3K4me3 at ICR of maternal imprinting genes which persists to 8-cell embryos and is associated with increased expression from maternal allele in Cwt+Mmut+Pwt embryos. Aberrant H3K27me3 is still retained in these Cwt+Mmut+Pwt embryos.

  13. Supplementary Fig. 13 Original uncropped gel of Supplementary Fig. 2b.

    Boxes indicate the cropped regions in Supplementary Fig. 2b.

Supplementary information

  1. Supplementary Information

    Supplementary Figs. 1–13

  2. Reporting Summary

  3. Supplementary Table 1

    Sequencing information of STAR ChIP-seq.

  4. Supplementary Table 2

    Genes with allele specific H3K36me3 in mouse early embryos.

  5. Supplementary Table 3

    Differential expressed genes in Dnmt3L control and knock out fullgrown oocyte.

  6. Supplementary Table 4

    Differentially expressed genes in control and Setd2mNull fullgrown oocyte.

  7. Supplementary Table 5

    Primers and sgRNAs used in this study.

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https://doi.org/10.1038/s41588-019-0398-7