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

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 Lhx8induced 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.

Cell landscape of larval and adult Xenopus laevis at single-cell resolution

“…The rapid development of high-throughput single-cell RNA sequencing (scRNA-seq) technology offer a good opportunity to dissect cell heterogeneity of Xenopus , from embryogenesis 1 , 2 to individual organs such as cornea and kidney 3 , 4 , and to reveal the cellular mechanism of Xenopus regeneration such as in limb 5 , 6 , tail 7 , 8 and spinal cord 9 . A large number of organism-wide single-cell atlases have been constructed for various species, such as Homo sapiens 10 , Macaca fascicularis 11 , Mus musculus 12 , Danio rerio 13 , Drosophila melanogaster 14 , Ciona intestinalis 15 , Caenorhabditis elegans 16 , Schmidtea mediterranea 17 , and Stylophora pistillata 18 .…”

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

“…The genomic resources generated here will thus provide important tools for further studies. Given the crucial role of X. tropicalis for genomic analysis of development and regeneration 114,115 , the improvements to our understanding of its genome reported here will provide a more finely grained view of biomedically important genetic and epigenetic mechanisms. This new genome is also important from the standpoint of evolutionary genomics, as comparisons between the genomes of X. tropicalis and X. laevis shed light on mechanisms of genome duplication 115 .…”

Temporal transcriptomic profiling reveals dynamic changes in gene expression of Xenopus animal cap upon activin treatment

“…During the blastula stage of embryonic development, zygotic gene activation occurs, which is called the mid-blastula transition (MBT) 53 , 54 . It has been reported that the open chromatin accessibility for gene expression becomes higher after MBT (at least after stage 9) in Xenopus ACs 55 . Our transcriptome data using ACs dissected from blastula demonstrated the dynamic expression of various epigenetic regulators, which increase chromatin accessibility and lead to acceleration of gene transcription.…”