Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo

Joakim Palovaara, Shunsuke Saiga, Jos R. Wendrich, Nicole Van 'T Wout Hofland, J.P. van Schayck, Friederike Hater, Sumanth Mutte, Jouke Sjollema, Mark Boekschoten, Guido J. Hooiveld, Dolf Weijers*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

60 Citations (Scopus)


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-Snd 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.
Original languageEnglish
Pages (from-to)894-904
JournalNature Plants
Issue number11
Publication statusPublished - 1 Nov 2017


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