ArticleDevelopmental biology2017
Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula.
Article in Developmental biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 46 citations in OpenAlex.
- Review
- Sox8 is essential for vertebrate gastrulation.EMBO reports · 2025Article
- A network of transient domains for breaking symmetry during anterior-posterior axis formation in the porcine embryo.Developmental dynamics : an official publication of the American Association of Anatomists · 2025Article
- Double assurance in the induction of axial development by egg dorsal determinants inProceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Temporal Transcriptomic Profiling of the DevelopingbioRxiv : the preprint server for biology · 2024Article
- Cell lineage-guided mass spectrometry reveals increased energy metabolism and reactive oxygen species in the vertebrate organizer.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Intestinal Paneth cell differentiation relies on asymmetric regulation of Wnt signaling by Daam1/2.Science advances · 2023Article
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- Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions.BMC genomics · 2022Article
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- Temporal transcriptomic profiling reveals dynamic changes in gene expression of Xenopus animal cap upon activin treatment.Scientific reports · 2021Article
- Expression patterns of signalling molecules and transcription factors in the early rabbit embryo and their significance for modelling amniote axis formation.Development genes and evolution · 2021Article
- A temporally resolved transcriptome for developing "Keller" explants of the Xenopus laevis dorsal marginal zone.Developmental dynamics : an official publication of the American Association of Anatomists · 2021Article
- Purified Bighead protein efficiently promotes head development in the South African clawed frog,microPublication biology · 2021Article
- T-Cell Factors as Transcriptional Inhibitors: Activities and Regulations in Vertebrate Head Development.Frontiers in cell and developmental biology · 2021Review
- Neural crest multipotency and specification: power and limits of single cell transcriptomic approaches.Faculty reviews · 2021Review
- The extracellular matrix in development.Development (Cambridge, England) · 2020Review
- Transcriptomics and Proteomics Methods forCold Spring Harbor protocols · 2020Article
- Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. Here we present a deep RNA-seq dataset of transcripts expressed in dorsal and ventral lips of the early Xenopus gastrula embryo using the new genomic information, which was further annotated by blast searches against the human proteome. Overall, our findings confirm previous results from differential screenings using other methods that uncovered classical dorsal genes such as Chordin, Noggin and Cerberus, as well as ventral genes such as Sizzled, Ventx, Wnt8 and Bambi. Complete transcriptome-wide tables of mRNAs suitable for data mining are presented, which include many novel dorsal- and ventral-specific genes. RNA-seq was very quantitative and reproducible, and allowed us to define dorsal and ventral signatures useful for gene set expression analyses (GSEA). As an example of a new gene, we present here data on an organizer-specific secreted protein tyrosine kinase known as Pkdcc (protein kinase domain containing, cytoplasmic) or Vlk (vertebrate lonesome kinase). Overexpression experiments indicate that Pkdcc can act as a negative regulator of Wnt/ β-catenin signaling independently of its kinase activity. We conclude that RNA-Seq in combination with the X. laevis complete genome now available provides a powerful tool for unraveling cell-cell signaling pathways during embryonic induction.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.