Dynamic CpG island methylation landscape in oocytes and preimplantation embryos

Abstract

Elucidating how and to what extent CpG islands (CGIs) are methylated in germ cells is essential to understand genomic imprinting and epigenetic reprogramming1,2,3. Here we present, to our knowledge, the first integrated epigenomic analysis of mammalian oocytes, identifying over a thousand CGIs methylated in mature oocytes. We show that these CGIs depend on DNMT3A and DNMT3L4,5 but are not distinct at the sequence level, including in CpG periodicity6. They are preferentially located within active transcription units and are relatively depleted in H3K4me3, supporting a general transcription-dependent mechanism of methylation. Very few methylated CGIs are fully protected from post-fertilization reprogramming but, notably, the majority show incomplete demethylation in embryonic day (E) 3.5 blastocysts. Our study shows that CGI methylation in gametes is not entirely related to genomic imprinting but is a strong factor in determining methylation status in preimplantation embryos, suggesting a need to reassess mechanisms of post-fertilization demethylation.

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Figure 1: DNA methylation landscape in oocytes and sperm determined by RRBS.
Figure 2: Mechanism of DNA methylation establishment in oocytes.
Figure 3: Biological significance and fate of CGI methylation in oocytes.

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Acknowledgements

We thank K. Tabbada for technical assistance with Illumina sequencing, H. Mertani, P. Mollard, W. Dean and W. Reik for input and discussions and M. Branco and W. Reik for making available the DNMT3A conditional knockout line. This work was supported by grants G0800013 and G0801156 from the Medical Research Council to G.K. and by the Biotechnology and Biological Sciences Research Council. S.A.S. was supported by the Babraham Institute and the Centre for Trophoblast Research.

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Contributions

S.A.S. designed the study, performed RRBS, mRNA-Seq, direct BS-PCR experiments, data analysis and wrote the manuscript. S.-i.T. contributed to direct bisulphite sequencing PCR experiments and performed oocyte collections. F.K. and S.R.A. performed CpG methylation calls, general Illumina sequence alignments and data analysis. N.R. performed ChIP-Seq experiments. N.C. analyzed data. A.S.-P. performed statistical analysis. S.S. and K.H. provided Dnmt3L wild-type and knockout oocytes. G.K. designed and supervised the study and wrote the manuscript.

Corresponding author

Correspondence to Gavin Kelsey.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–9 and Supplementary Tables 2–4. (PDF 4729 kb)

Supplementary Table 1

CpG Island methylation calls (separate Excel file). (XLSX 13157 kb)

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Smallwood, S., Tomizawa, S., Krueger, F. et al. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat Genet 43, 811–814 (2011). https://doi.org/10.1038/ng.864

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