During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered—in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue- and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.

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A correction to this article is available online at https://doi.org/10.1038/s41477-017-0077-6.

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  • 11 January 2018

    In the version of this Resource originally published, the author information was incorrect. Jos R. Wendrich should have had a present address: Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, 9052 Ghent, Belgium. Mark Boekschoten and Guido J. Hooiveld should have been affiliated to the Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE Wageningen, The Netherlands. In addition, the version of Supplementary Table 5 originally published with this Resource was not the intended final version and included inaccurate citations to the display items of the Resource, and the file format and extension did not match. These errors have now been corrected in all versions of the Resource.


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The authors thank T. Laux, R. Deal and S. Henikoff for sharing materials. Further, the authors thank the students M. Geerlings, D. van der Plaat, E. Asamoah Gyimah, M. Goranova, A. Kuhn, L. van der Bent, I. Papakosta, S. Thomaidou, S. Hedžet and K. Heidemeyer for their contributions. This study was supported by the Federation of European Biochemical Societies (FEBS) (J.P.), ERA-CAPS project EURO-PEC (grant number 849.13.006) and the European Research Council (ERC Starting Grant ‘CELLPATTERN’; contract number 281573 to D.W.).

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Author notes

  1. Joakim Palovaara and Shunsuke Saiga contributed equally to this work.


  1. Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands

    • Joakim Palovaara
    • , Shunsuke Saiga
    • , Jos R. Wendrich
    • , Nicole van ‘t Wout Hofland
    • , J. Paul van Schayck
    • , Friederike Hater
    • , Sumanth Mutte
    • , Jouke Sjollema
    •  & Dolf Weijers
  2. Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands

    • Mark Boekschoten
    •  & Guido J. Hooiveld
  3. Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium

    • Jos R. Wendrich


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D.W. conceived the study; J.P., S.S., J.R.W. and D.W. designed research; S.S. generated INTACT lines; J.P. and N.v.W.H. optimized and adapted experimental set-up; J.P., S.S. and J.R.W. performed INTACT; F.H. and J.P. performed nuclear versus cellular RNA comparison; M.B., G.J.H. and J.P. performed transcriptomic profiling and analysed data with support from S.M.; J.P., S.S., J.R.W., J.P.v.S. and J.S. validated expression patterns; J.P.v.S. and J.P. designed and developed the AlBERTO browser; J.P. and D.W. wrote the paper with input from all other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Dolf Weijers.

Supplementary information

  1. Supplementary Information

    Supplementary Figures 1–12, Supplementary Tables 1–3, Supplementary References.

  2. Life Sciences Reporting Summary

  3. Supplementary Table 4

    Linear correlation and residual analysis of nuclear and cellular whole-genome expression.

  4. Supplementary Table 5

    The atlas data set.

  5. Supplementary Table 6

    Comparison of seed tissue contamination in INTACT- and FANS-generated nuclear transcriptomes.

  6. Supplementary Table 7

    List of primers used for cloning and quantitative RT-PCR.

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