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Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

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Mammalian pre-implantation development is a complex process involving dramatic changes in the transcriptional architecture1,2,3,4. We report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos, using single-cell RNA sequencing. Based on single-nucleotide variants in human blastomere messenger RNAs and paternal-specific single-nucleotide polymorphisms, we identify novel stage-specific monoallelic expression patterns for a significant portion of polymorphic gene transcripts (25 to 53%). By weighted gene co-expression network analysis5,6, we find that each developmental stage can be delineated concisely by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation and metabolism, acting in a step-wise fashion from cleavage to morula. Cross-species comparisons with mouse pre-implantation embryos reveal that the majority of human stage-specific modules (7 out of 9) are notably preserved, but developmental specificity and timing differ between human and mouse. Furthermore, we identify conserved key members (or hub genes) of the human and mouse networks. These genes represent novel candidates that are likely to be key in driving mammalian pre-implantation development. Together, the results provide a valuable resource to dissect gene regulatory mechanisms underlying progressive development of early mammalian embryos.

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Figure 1: High-resolution single-cell transcriptome analysis of human pre-implantation embryos.
Figure 2: Tracing parent-of-origin allelic RNA transcripts through SNV analysis in pre-implantation embryos.
Figure 3: Network analysis of human pre-implantation development.
Figure 4: Stage-specific gene activation is preserved in human and mouse pre-implantation development.

Change history

  • 29 August 2013

    Ref. 26 and the associated sentence in the text were corrected; two reference citations in the online Methods were corrected.


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We thank many of our colleagues for invaluable discussions and comments on our study, in particular, P. Pajukanta at UCLA for very helpful suggestions on SNP analyses and D. Geschwind for critically reading the manuscript. This work was supported by 973 Grant Programs 2012CB966300, 2011CB966204 and 2011CB965102 from the Ministry of Science and Technology in China; the International Science and Technology Cooperation Program of China (no. 2011DFB30010); and the National Natural Science Foundation of China (81271258).

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Authors and Affiliations



Z.X., K.H., J.L. and G.F. designed the study. Z.X., L.C., C.J., Y.F., Z.L., Q.Z., L.C. and Y.E.S. carried out experiments or contributed critical reagents and protocols. K.H., C.C. and S.H. analysed the data and performed statistical analyses. K.H. and G.F. wrote the manuscript in discussion with all the authors. All the authors read and approved the manuscript.

Corresponding authors

Correspondence to Zhigang Xue, Jia-yin Liu or Guoping Fan.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Text, Supplementary Figures 1-9 and Supplementary References. (PDF 884 kb)

Supplementary Table 1

This file contains single-cell RNA-Seq statistics. (XLS 20 kb)

Supplementary Table 2

This file contains inferred Haplotype blocks as described in the methods. (XLS 52 kb)

Supplementary Table 3

This file contains a summary of hub gene data sets. (XLS 56 kb)

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Xue, Z., Huang, K., Cai, C. et al. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature 500, 593–597 (2013).

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