Abstract
Primary germ layers have the potential to form all tissues in the mature organism, and their formation during gastrulation requires precise epigenetic modulation of both proximal and distal regulatory elements. Previous studies indicated that spatial and temporal patterns of gene expression in the gastrula predispose individual regions to distinct cell fates. However, the underlying epigenetic mechanisms remain largely unexplored. Here, we profile the spatiotemporal landscape of the epigenome and transcriptome of the mouse gastrula. We reveal the asynchronous dynamics of proximal chromatin states during germ layer formation as well as unique gastrula-specific epigenomic features of regulatory elements, which have strong usage turnover dynamics and clear germ layer-specific signatures. Importantly, we also find that enhancers around organogenetic genes, which are weakly expressed at the gastrulation stage, are frequently pre-marked by histone H3 lysine 27 acetylation (H3K27ac) in the gastrula. By using the transgenic mice and genome editing system, we demonstrate that a pre-marked enhancer, which is located in the intron of a brain-specific gene 2510009E07Rik, exhibits specific enhancer activity in the ectoderm and future brain tissue, and also executes important function during mouse neural differentiation. Taken together, our study provides the comprehensive epigenetic information for embryonic patterning during mouse gastrulation, demonstrates the importance of gastrula pre-marked enhancers in regulating the correct development of the mouse embryo, and thus broadens the current understanding of mammalian embryonic development and related diseases.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Wolpert, L., Tickle, C. & Martinez-Arias, A. Principles of Development. Fifth edn (Oxford, UK: Oxford University Press, 2015).
Arnold, S. J. & Robertson, E. J. Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo. Nat. Rev. Mol. Cell. Biol. 10, 91–103 (2009).
Tam, P. P. & Behringer, R. R. Mouse gastrulation: the formation of a mammalian body plan. Mech. Dev. 68, 3–25 (1997).
Downs, K. M. & Davies, T. Staging of gastrulating mouse embryos by morphological landmarks in the dissecting microscope. Development 118, 1255–1266 (1993).
Takaoka, K. & Hamada, H. Cell fate decisions and axis determination in the early mouse embryo. Development 139, 3–14 (2012).
Benitah, S. A. & Frye, M. Stem cells in ectodermal development. J. Mol. Med. 90, 783–790 (2012).
Tada, S. et al. Characterization of mesendoderm: a diverging point of the definitive endoderm and mesoderm in embryonic stem cell differentiation culture. Development 132, 4363–4374 (2005).
Brand, T. Heart development: molecular insights into cardiac specification and early morphogenesis. Dev. Biol. 258, 1–19 (2003).
Atlasi, Y. & Stunnenberg, H. G. The interplay of epigenetic marks during stem cell differentiation and development. Nat. Rev. Genet. 18, 643–658 (2017).
Liu, C., Peng, G. & Jing, N. TGF-beta signaling pathway in early mouse development and embryonic stem cells. Acta. Biochim. Biophys. Sin. 50, 68–73 (2018).
Liu, X. et al. Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. Nature 537, 558–562 (2016).
Dahl, J. A. et al. Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. Nature 537, 548–552 (2016).
Wu, J. et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature 534, 652–657 (2016).
Ke, Y. et al. 3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis. Cell 170, 367–381 (2017).
Wang, C. et al. Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development. Nat. Cell. Biol. 20, 620–631 (2018).
Zylicz, J. J. et al. G9a regulates temporal preimplantation developmental program and lineage segregation in blastocyst. Elife 7, pii: e33361 (2018).
Zylicz, J. J. et al. Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development. Elife 4, pii: e09571 (2015).
Gorkin, D. U. et al. Systematic mapping of chromatin state landscapes during mouse development. BioRxiv 2017. https://doi.org/10.1101/166652
Nord, A. S. et al. Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell 155, 1521–1531 (2013).
Yang, X. et al. Silencing of developmental genes by H3K27me3 and DNA methylation reflects the discrepant plasticity of embryonic and extraembryonic lineages. Cell. Res. 28, 593–596 (2018).
Smith, Z. D. et al. Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature 549, 543–547 (2017).
Adam, R. C. et al. Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice. Nature 521, 366–370 (2015).
Ong, C. T. & Corces, V. G. Enhancers: emerging roles in cell fate specification. EMBO Rep. 13, 423–430 (2012).
Wang, A. et al. Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates. Cell Stem Cell 16, 386–399 (2015).
Tam, P. P. & Loebel, D. A. Gene function in mouse embryogenesis: get set for gastrulation. Nat. Rev. Genet. 8, 368–381 (2007).
Peng, G. et al. Spatial transcriptome for the molecular annotation of lineage fates and cell identity in mid-gastrula mouse embryo. Dev. Cell. 36, 681–697 (2016).
Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931–21936 (2010).
Roadmap Epigenomics, C. et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317–330 (2015).
Charlet, J. et al. Bivalent regions of cytosine methylation and H3K27 acetylation suggest an active role for DNA methylation at enhancers. Mol. Cell 62, 422–431 (2016).
De Gobbi, M. et al. Generation of bivalent chromatin domains during cell fate decisions. Epigenetics Chromatin 4, 9 (2011).
Kojima, Y. et al. The transcriptional and functional properties of mouse epiblast stem cells resemble the anterior primitive streak. Cell Stem Cell 14, 107–120 (2014).
Whyte, W. A. et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 482, 221–225 (2012).
Osterwalder, M. et al. Enhancer redundancy provides phenotypic robustness in mammalian development. Nature 554, 239–243 (2018).
Shen, H. et al. Suppression of enhancer overactivation by a RACK7-histone demethylase complex. Cell 165, 331–342 (2016).
Strumpf, D. et al. Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development 132, 2093–2102 (2005).
Jiang, B. & Mendelson, C. R. USF1 and USF2 mediate inhibition of human trophoblast differentiation and CYP19 gene expression by Mash-2 and hypoxia. Mol. Cell. Biol. 23, 6117–6128 (2003).
Nagai, T. et al. The expression of the mouse Zic1, Zic2, and Zic3 gene suggests an essential role for Zic genes in body pattern formation. Dev. Biol. 182, 299–313 (1997).
Wu, G. & Scholer, H. R. Role of Oct4 in the early embryo development. Cell. Regen. 3, 7 (2014).
Mesman, S. & Smidt, M. P. Tcf12 is involved in early cell-fate determination and subset specification of midbrain dopamine neurons. Front. Mol. Neurosci. 10, 353 (2017).
Bonev, B. et al. Multiscale 3D genome rewiring during mouse neural development. Cell 171, 557–572 (2017).
Yue, F. et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature 515, 355–364 (2014).
Dickel, D. E. et al. Ultraconserved enhancers are required for normal development. Cell 172, 491–499 (2018).
Zhang, K. et al. Distinct functions of BMP4 during different stages of mouse ES cell neural commitment. Development 137, 2095–2105 (2010).
Nichols, J. & Smith, A. Naive and primed pluripotent states. Cell Stem Cell 4, 487–492 (2009).
Smith, A. Formative pluripotency: the executive phase in a developmental continuum. Development 144, 365–373 (2017).
Kubo, A. et al. Development of definitive endoderm from embryonic stem cells in culture. Development 131, 1651–1662 (2004).
Cheng, X. et al. Self-renewing endodermal progenitor lines generated from human pluripotent stem cells. Cell Stem Cell 10, 371–384 (2012).
Kumar, N. et al. Generation of an expandable intermediate mesoderm restricted progenitor cell line from human pluripotent stem cells. Elife 4, pii: e08413 (2015).
Liu, C. et al. Suppressing nodal signaling activity predisposes ectodermal differentiation of epiblast stem cells. Stem Cell Rep. 11, 43–57 (2018).
Du, Z. et al. Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature 547, 232–235 (2017).
Zhang, Y. et al. Dynamic epigenomic landscapes during early lineage specification in mouse embryos. Nat. Genet. 50, 96–105 (2018).
Zhu, J. et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152, 642–654 (2013).
Rossant., J. & Tam., P. P. L. Mouse Development: Patterning, Morphogenesis, and Organogenesis. (San Diego, USA: Gulf Professional Publishing, 2002).
Edlund, T. & Jessell, T. M. Progression from extrinsic to intrinsic signaling in cell fate specification: a view from the nervous system. Cell 96, 211–224 (1999).
Bogdanovic, O. et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat. Genet. 48, 417–426 (2016).
Cusanovich, D. A. et al. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature 555, 538–542 (2018).
Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015).
Hainer, S. J., Boskovic, A., McCannell, K. N., Rando, O. J. & Fazzio, T. G. Profiling of pluripotency factors in single cells and early embryos. Cell 177, 1319–1329 (2019).
Behringer, R. R., Gertsenstein, M., Nagy, K. V. & Nagy, A. Manipulating the mouse embryo: a laboratory manual. (New York, USA: Cold Spring Harbor Laboratory Press, 2014).
Chen, J. et al. Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq. Nat. Protoc. 12, 566–580 (2017).
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
Anders, S., Pyl, P. T. & Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Leek, J. T., Johnson, W. E., Parker, H. S., Jaffe, A. E. & Storey, J. D. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 28, 882–883 (2012).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
Landt, S. G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome. Res. 22, 1813–1831 (2012).
Guo, H. et al. Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing. Nat. Protoc. 10, 645–659 (2015).
Ernst, J. & Kellis, M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods 9, 215–216 (2012).
McLean, C. Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495–501 (2010).
Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L. A. VISTA Enhancer Browser - a database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88–D92 (2007).
Ran, F. A. et al. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8, 2281 (2013).
Acknowledgements
We thank Drs Patrick Tam, Chi-chung Hui, Bing Zhu and Dangsheng Li for helpful advice and discussion. We thank Dr Bin Zhou for the generous gift of the pHsp68-LacZ plasmid. This work was supported in part by the National Key Basic Research and Development Program of China (2018YFA0800100, 2018YFA0108000, 2018YFA0107200, 2017YFA0102700, 2014CB964804, 2018YFA0107601 and 2015CB964500), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16020501 and XDA16020404), the Genome Tagging Project, and the National Natural Science Foundation of China (31900454, 31501178, 31430058, 31571513, 31630043, 31871456, 91519314, 31661143042, 81561138005, 31625018, 81521002, 31530048, 81672117 and 31730062), and Shanghai Municipal Commission for Science and Technology (17JC1400900 and 17411954900).
Author information
Authors and Affiliations
Contributions
Y. Qiao, J.L., F.T., and N.J. conceived and supervised the project. X.Y., J.L., Y.C., Y. Qian, S.F., F.Y., H.X., and Y.H. performed the experiments. B.H., J.D., Y.H., and R.W. performed the computational analyses. X.Y., B.H., Y. Qiao, G.P., F.T, and N.J wrote the paper with the help from all other authors.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Supplementary information
Rights and permissions
About this article
Cite this article
Yang, X., Hu, B., Liao, J. et al. Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development. Cell Res 29, 911–926 (2019). https://doi.org/10.1038/s41422-019-0234-8
Received:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/s41422-019-0234-8
This article is cited by
-
Single-cell multi-omics delineates the dynamics of distinct epigenetic codes coordinating mouse gastrulation
BMC Genomics (2025)
-
Genomic locus of lncRNA-Gm26793 forms an inter-chromosomal interaction with Cubn to ensure proper stem cell differentiation in vitro and in vivo
Cell Discovery (2025)
-
Alternative splicing dynamics during gastrulation in mouse embryo
Scientific Reports (2025)
-
Base editing-mediated one-step inactivation of the Dnmt gene family reveals critical roles of DNA methylation during mouse gastrulation
Nature Communications (2023)
-
Epigenetic reorganization during early embryonic lineage specification
Genes & Genomics (2022)
