Article | Published:

The landscape of accessible chromatin in mammalian preimplantation embryos

Nature volume 534, pages 652657 (30 June 2016) | Download Citation

Abstract

In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development.

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Primary accessions

Gene Expression Omnibus

Data deposits

All data have been deposited to GEO with the accession number GSE66390.

References

  1. 1.

    Chromatin modifications and their function. Cell 128, 693–705 (2007)

  2. 2.

    & Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57, 159–197 (1988)

  3. 3.

    & Mapping human epigenomes. Cell 155, 39–55 (2013)

  4. 4.

    & Chromatin dynamics in the regulation of cell fate allocation during early embryogenesis. Nat. Rev. Mol. Cell Biol. 15, 723–735 (2014)

  5. 5.

    , & Making a firm decision: multifaceted regulation of cell fate in the early mouse embryo. Nat. Rev. Genet. 10, 467–477 (2009)

  6. 6.

    , , , & Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013)

  7. 7.

    et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015)

  8. 8.

    et al. Epigenetics. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910–914 (2015)

  9. 9.

    et al. Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment. Cell 159, 1312–1326 (2014)

  10. 10.

    et al. Immunogenetics. Chromatin state dynamics during blood formation. Science 345, 943–949 (2014)

  11. 11.

    et al. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol. 17, 41 (2016)

  12. 12.

    , , & Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343, 193–196 (2014)

  13. 13.

    et al. CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res. 22, 2399–2408 (2012)

  14. 14.

    et al. ETV6 fusion genes in hematological malignancies: a review. Leuk. Res. 36, 945–961 (2012)

  15. 15.

    & Genomic imprinting: parental influence on the genome. Nat. Rev. Genet. 2, 21–32 (2001)

  16. 16.

    et al. Programming and inheritance of parental DNA methylomes in mammals. Cell 157, 979–991 (2014)

  17. 17.

    et al. Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors. Nat. Biotechnol. 33, 769–774 (2015)

  18. 18.

    , , & RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat. Struct. Mol. Biol. 15, 71–78 (2008)

  19. 19.

    & A new direction for gene looping. Dev. Cell 23, 919–921 (2012)

  20. 20.

    et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116–120 (2012)

  21. 21.

    et al. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 7, 597–606 (2004)

  22. 22.

    & Retrotransposons shape species-specific embryonic stem cell gene expression. Retrovirology 12, 45 (2015)

  23. 23.

    et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat. Genet. 45, 836–841 (2013)

  24. 24.

    & Enhancers as information integration hubs in development: lessons from genomics. Trends Genet. 28, 276–284 (2012)

  25. 25.

    et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495–501 (2010)

  26. 26.

    et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010)

  27. 27.

    , , , & The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification. Nat. Cell Biol. 16, 516–528 (2014)

  28. 28.

    et al. Targeted mutagenesis of the transcription factor GATA-4 gene in mouse embryonic stem cells disrupts visceral endoderm differentiation in vitro. Development 121, 3877–3888 (1995)

  29. 29.

    et al. GATA6 regulates HNF4 and is required for differentiation of visceral endoderm in the mouse embryo. Genes Dev. 12, 3579–3590 (1998)

  30. 30.

    et al. HIPPO pathway members restrict SOX2 to the inner cell mass where it promotes ICM fates in the mouse blastocyst. PLoS Genet. 10, e1004618 (2014)

  31. 31.

    , , , & Maternal-zygotic knockout reveals a critical role of Cdx2 in the morula to blastocyst transition. Dev. Biol. 398, 147–152 (2015)

  32. 32.

    et al. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol. Syst. Biol. 6, 377 (2010)

  33. 33.

    et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134–1148 (2013)

  34. 34.

    , , , & Nuclear receptor NR5A2 is required for proper primitive streak morphogenesis. Dev. Dyn. 235, 3359–3369 (2006)

  35. 35.

    et al. Orphan nuclear receptor LRH-1 is required to maintain Oct4 expression at the epiblast stage of embryonic development. Mol. Cell. Biol. 25, 3492–3505 (2005)

  36. 36.

    The molecular foundations of the maternal to zygotic transition in the preimplantation embryo. Hum. Reprod. Update 8, 323–331 (2002)

  37. 37.

    , & Regulation of transcriptional activity during the first and second cell cycles in the preimplantation mouse embryo. Dev. Biol. 181, 296–307 (1997)

  38. 38.

    , , & Dynamics of global gene expression changes during mouse preimplantation development. Dev. Cell 6, 117–131 (2004)

  39. 39.

    et al. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature 487, 57–63 (2012)

  40. 40.

    et al. Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly. Nat. Struct. Mol. Biol. 22, 662–671 (2015)

  41. 41.

    et al. The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3′ processing. EMBO J. 34, 1523–1537 (2015)

  42. 42.

    et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protocols 9, 171–181 (2014)

  43. 43.

    et al. TELP, a sensitive and versatile library construction method for next-generation sequencing. Nucleic Acids Res. 43, e35 (2015)

  44. 44.

    et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477, 289–294 (2011)

  45. 45.

    et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013)

  46. 46.

    et al. Deterministic and stochastic allele specific gene expression in single mouse blastomeres. PLoS One 6, e21208 (2011)

  47. 47.

    et al. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 148, 816–831 (2012)

  48. 48.

    , & HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015)

  49. 49.

    et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, 3 (2003)

  50. 50.

    et al. Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol. 6, R33 (2005)

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Acknowledgements

We appreciate B. Ren, D. Leung, H. Yang and the members of the Xie laboratory for comments during preparation of the manuscript. This work is supported by the funding provided by the National Basic Research Program of China (973 program) 2015CB856201 (W.Xie), the National Natural Science Foundation of China 31422031 (W.Xie), 31171381 (J.N.), 81472855 (X.Y.), the National Basic Research Program of China 2012CB966701 (J.N.), the Beijing Natural Science Foundation grant 5152014 (J.N.), Tsinghua University Initiative Scientific Research Program (20131089278, 2014z21046) (X.Y.), the funding from the THU-PKU Center for Life Sciences (W.Xie, X.Y.), and the Youth Thousand Scholar Program of China (W.Xie, X.Y.).

Author information

Author notes

    • Jingyi Wu
    •  & Bo Huang

    These authors contributed equally to this work.

Affiliations

  1. MOE Key Laboratory of Bioinformatics, Center for Stem Cell Biology and Regenerative Medicine, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China

    • Jingyi Wu
    • , Qiangzong Yin
    • , Yunlong Xiang
    • , Bingjie Zhang
    • , Bofeng Liu
    • , Qiujun Wang
    • , Weikun Xia
    • , Yuanyuan Li
    • , Jing Ma
    • , Hui Zheng
    • , Wenhao Zhang
    •  & Wei Xie
  2. Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China

    • Jingyi Wu
    • , Yang Liu
    • , Xuerui Yang
    •  & Wei Xie
  3. PKU-THU Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China

    • Bo Huang
  4. Joint Graduate Program of Peking-Tsinghua-NIBS, College of Life Sciences, Peking University, Beijing 100871, China

    • He Chen
  5. MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China

    • Yang Liu
    •  & Xuerui Yang
  6. Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China

    • Wenzhi Li
    • , Jia Ming
    •  & Jie Na
  7. Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore 117609, Singapore

    • Xu Peng
    •  & Feng Xu
  8. School of Life Sciences, Tsinghua University, Beijing 100084, China

    • Jing Zhang
    •  & Zai Chang
  9. School of Medicine, Tsinghua University, Beijing 100084, China

    • Geng Tian
  10. Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore

    • Feng Xu

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Contributions

J.W., B.H. and W.Xie conceived and designed the experiments. J.W. conducted the ATAC-seq experiments. J.W., B.L., W.Xia and Q.W. developed CARM. B.H. performed the mouse embryo experiments with help from Y.X., J.M., W.L. and J.Z. H.C. prepared the RNA-seq libraries. Q.Y. and W.Z. helped with various experiments. J.W., H.C., H.Z., Y.L., X.Y. and W.Xie performed the bioinformatics analysis of the data. B.Z. conducted the ChIP-seq experiment. X.P., F.X., G.T. advised the development or application of ATAC-seq and CARM. Y.L. and Q.W. performed NGS sequencing. Z.C. and J.N. supervised the mouse work. J.W., H.C., B.H. and W.Xie wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Wei Xie.

Reviewer Information Nature thanks T. Magnuson and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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https://doi.org/10.1038/nature18606

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