Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates

EMBO J. 2021 May 3;40(9):e104913. doi: 10.15252/embj.2020104913. Epub 2021 Feb 8.


During vertebrate gastrulation, mesoderm is induced in pluripotent cells, concomitant with dorsal-ventral patterning and establishing of the dorsal axis. We applied single-cell chromatin accessibility and transcriptome analyses to explore the emergence of cellular heterogeneity during gastrulation in Xenopus tropicalis. Transcriptionally inactive lineage-restricted genes exhibit relatively open chromatin in animal caps, whereas chromatin accessibility in dorsal marginal zone cells more closely reflects transcriptional activity. We characterized single-cell trajectories and identified head and trunk organizer cell clusters in early gastrulae. By integrating chromatin accessibility and transcriptome data, we inferred the activity of transcription factors in single-cell clusters and tested the activity of organizer-expressed transcription factors in animal caps, alone or in combination. The expression profile induced by a combination of Foxb1 and Eomes most closely resembles that observed in the head organizer. Genes induced by Eomes, Otx2, or the Irx3-Otx2 combination are enriched for maternally regulated H3K4me3 modifications, whereas Lhx8-induced genes are marked more frequently by zygotically controlled H3K4me3. Taken together, our results show that transcription factors cooperate in a combinatorial fashion in generally open chromatin to orchestrate zygotic gene expression.

Keywords: cell trajectories; chromatin accessibility; mesendoderm; organizer; transcription factors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Body Patterning
  • Chromatin / genetics*
  • Chromatin / metabolism
  • Gastrulation
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental
  • Sequence Analysis, RNA
  • Single-Cell Analysis / methods*
  • Transcription Factors / metabolism*
  • Xenopus / embryology*
  • Xenopus / genetics
  • Xenopus Proteins / genetics*
  • Xenopus Proteins / metabolism


  • Chromatin
  • Transcription Factors
  • Xenopus Proteins

Associated data

  • GEO/GSE145619