Gene expression variation in Arabidopsis embryos at single-nucleus resolution

Ping Kao, Michael A. Schon, Magdalena Mosiolek, Balaji Enugutti, Michael D. Nodine*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)


Soon after fertilization of egg and sperm, plant genomes become transcriptionally activated and drive a series of coordinated cell divisions to form the basic body plan during embryogenesis. Early embryonic cells rapidly diversify from each other, and investigation of the corresponding gene expression dynamics can help elucidate underlying cellular differentiation programs. However, current plant embryonic transcriptome datasets either lack cell-specific information or have RNA contamination from surrounding non-embryonic tissues. We have coupled fluorescence-activated nuclei sorting together with single-nucleus mRNA-sequencing to construct a gene expression atlas of Arabidopsis thaliana early embryos at single-cell resolution. In addition to characterizing cell-specific transcriptomes, we found evidence that distinct epigenetic and transcriptional regulatory mechanisms operate across emerging embryonic cell types. These datasets and analyses, as well as the approach we devised, are expected to facilitate the discovery of molecular mechanisms underlying pattern formation in plant embryos.

Original languageEnglish
Article numberdev199589
JournalDevelopment (Cambridge)
Issue number13
Publication statusPublished - 6 Jul 2021


  • Arabidopsis
  • Embryo
  • Epigenetic
  • Gene expression
  • Single-nucleus RNA-seq
  • Transcription factor


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