ArticleThe EMBO journal2021
Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates.
Article in The EMBO journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 34 citations in OpenAlex.
- CANTAC-seq analysis reveals E2f1 and Otx1 coordinate zygotic genome activation in Xenopus tropicalis.Nature communications · 2025Article
- Deletion upstream of MAB21L2 highlights the importance of evolutionarily conserved non-coding sequences for eye development.Nature communications · 2024Article
- The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model.Nucleic acids research · 2024Article
- Single-nucleus chromatin landscape dataset of mouse brain development and aging.Scientific data · 2024Article
- The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis.Nucleic acids research · 2024Article
- Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs.Nature communications · 2024Article
- Defining high confidence targets of differential CpG methylation in response to in utero arsenic exposure and implications for cancer risk.Toxicology and applied pharmacology · 2024Article
- Single-nucleus chromatin landscapes during zebrafish early embryogenesis.Scientific data · 2023Article
- Computational approaches to understand transcription regulation in development.Biochemical Society transactions · 2023Review
- Backup transcription factor binding sites protect human genes from mutations in the promoter.PloS one · 2023Article
- Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes reduces chromatin accessibility at promoters.Scientific reports · 2022Article
- Epigenomic dynamics of early Xenopus Embryos.Development, growth & differentiation · 2022Review
- The homeodomain transcription factor Ventx2 regulates respiratory progenitor cell number and differentiation timing during Xenopus lung development.Development, growth & differentiation · 2022Article
- Review
- Cell landscape of larval and adult Xenopus laevis at single-cell resolution.Nature communications · 2022Article
- Uncovering the mesendoderm gene regulatory network through multi-omic data integration.Cell reports · 2022Article
- Temporal transcriptomic profiling reveals dynamic changes in gene expression of Xenopus animal cap upon activin treatment.Scientific reports · 2021Article
- Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates.The EMBO journal · 2021Article
- Control of zygotic genome activation in Xenopus.Current topics in developmental biology · 2021Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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