Gene expression in dorsal halves of Apcdd1-depleted Xenopus laevis embryos
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ABSTRACT:
ORGANISM(S): Xenopus laevis
PROVIDER: GSE138834 | GEO | 2019/10/15
REPOSITORIES: GEO
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Project description:Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. Here, we use this wealth of knowledge as leverage in the design and analysis of a genomic visualization of organizer-related gene transcription. Using ectopic expression of the two major activities of the organizer, BMP and Wnt inhibition, as well as endogenous tissues, we generate a focused set of samples that represent different aspects of organizer signaling. The genomic expression values of each sample are then measured with oligonucleotide arrays. From this data, genes regulated by organizer signaling are selected and then clustered by their patterns of regulation. A new GO biological process annotation of the Xenopus genome allows us to rapidly identify clusters that are highly enriched for known gastrula patterning genes. Within these clusters, we can predict the expression patterns of unknown genes with remarkable accuracy, leading to the discovery of new organizer-related gastrula stage expression patterns for 19 genes. Moreover, the patterns of gene response observed within these clusters allow us to parse apart the contributions of BMP and Wnt inhibition in organizer function. We find that the majority of gastrula patterning genes respond transcriptionally to these activities according to only a few stereotyped patterns, allowing us to describe suites of genes that are likely to share similar regulatory mechanisms. These suites of genes demonstrate a mechanism where BMP inhibition initiates the organizer program before gastrulation, and Wnt inhibition maintains and drives the organizer program during gastrulation. Experiment Overall Design: In order to describe and separate the genomic expression changes induced by the two main organizing activities, BMP inhibition and Wnt inhibition, we created a panel of gastrula stage ventral tissues that ectopically overexpressed one or both of these activities, and compared these samples to endogenous dorsal and ventral gastrula stage tissue. Two well-studied organizer secreted factors, Noggin and Dickkopf-1 (Dkk-1), were used to ectopically inhibit BMP and Wnt signaling, respectively. Four different overexpression mixtures were injected ventrally into 4-cell embryos: noggin and eGFP (anti-BMP); noggin, dkk-1, and eGFP (anti-BMP and anti-Wnt); dkk-1 and eGFP (anti-Wnt); and eGFP alone. eGFP mRNA was used to trace targeting. Plasmid DNA was used for noggin and dkk-1 overexpression, instead of mRNA, in order to limit ectopic expression of these genes to post-MBT stages, more closely mimicking the endogenous regulation of these genes. The ventrally injected embryos were grown to early stage 10, sorted for appropriately targeted eGFP florescence, and then bisected between the dorsal and ventral halves at either stage 10 (early gastrula) or stage 11.5 (late gastrula). For the noggin and/or dkk-1 injected embryos, only the ventral halves of the embryos were saved, eliminating endogenous organizer tissues. For the embryos injected with only eGFP, both the ventral and dorsal halves were saved, creating separate ventral and dorsal control conditions. These five conditions were each generated twice at both stage 10 and 11.5, with each set of five samples coming from a single clutch of embryos, creating twenty total tissue samples from 4 different clutches. For each batch of injections some sorted embryos were allowed to develop through tailbud stages in order to validate the phenotypes induced by our constructs. Total RNA was then isolated from the twenty tissue samples and applied to Affymetrix oligonucleotide arrays.
2007-10-05 | E-GEOD-3368 | biostudies-arrayexpress
Project description:Animal embryos have the remarkable property of self-organization. Over 125 years ago Hans Driesch separated the two blastomeres of sea urchin embryos and obtained twins, in what was the foundational experiment of experimental embryology. Since then, embryonic twinning has been obtained experimentally in many animals by diverse methods. In a recent study, we developed bisection methods that generate identical twins reliably from Xenopus blastula embryos. In the present study we investigated the transcriptome of regenerating half-embryos after sagittal and dorsal-ventral (D-V) bisections. Individual embryos were operated at midblastula with an eyelash hair and cultured until early gastrula (stage 10.5) or late gastrula (Stage 12) and analyzed the transcriptome of each half-embryo by RNAseq. Because many genes are activated by wound healing, stringent analyses were used to identify genes upregulated in identical twins but not in either dorsal or ventral fragments. At early gastrula cell division-related genes such as histones were identified, whereas at late gastrula pluripotency genes (such as sox2) and germ layer determining genes (such as eomesodermin, ripply2 and activing receptor ACVRI) and a number of secretory pathway components (serpinH1, fucoleptin and sialyl transferase). These findings are consistent with a model in which cell division is required to heal damage, while maintaining pluripotency to permit formation of the organizer with a displacement of 900 from its original site. In addition, the extensive transcriptomic data presented here (30 RNA-seq libraries of individual whole or regenerating half-embryos) provides a useful resource for data mining gene expression during early vertebrate development.
2019-02-01 | GSE124563 | GEO
Project description:Gene expression in dorsal halves of Apcdd1-depleted Xenopus laevis embryos
| PRJNA577471 | ENA
Project description:Here we describe a base-resolution DNA methylation map of Xenopus laevis gastrula (st.10.5) embryos generated by whole genome bisulfite sequencing
2016-08-26 | GSE76247 | GEO
Project description:Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. Here, we use this wealth of knowledge as leverage in the design and analysis of a genomic visualization of organizer-related gene transcription. Using ectopic expression of the two major activities of the organizer, BMP and Wnt inhibition, as well as endogenous tissues, we generate a focused set of samples that represent different aspects of organizer signaling. The genomic expression values of each sample are then measured with oligonucleotide arrays. From this data, genes regulated by organizer signaling are selected and then clustered by their patterns of regulation. A new GO biological process annotation of the Xenopus genome allows us to rapidly identify clusters that are highly enriched for known gastrula patterning genes. Within these clusters, we can predict the expression patterns of unknown genes with remarkable accuracy, leading to the discovery of new organizer-related gastrula stage expression patterns for 19 genes. Moreover, the patterns of gene response observed within these clusters allow us to parse apart the contributions of BMP and Wnt inhibition in organizer function. We find that the majority of gastrula patterning genes respond transcriptionally to these activities according to only a few stereotyped patterns, allowing us to describe suites of genes that are likely to share similar regulatory mechanisms. These suites of genes demonstrate a mechanism where BMP inhibition initiates the organizer program before gastrulation, and Wnt inhibition maintains and drives the organizer program during gastrulation. Keywords: development, organizer, noggin, dkk-1, xenopus, gastrulation
2006-06-30 | GSE3368 | GEO
Project description:Transcriptional profiling of Xenopus laevis embryos and ectoderm (animal caps) comparing embryos injected with control morpholino with embryos injected with the morpholino mixture PVD2, which knocks down all three Xenopus PouV proteins. Whole embryos (WE) or animal caps (AC) were collected at late blastula (9) or early gastrula (10) stages from Control and PVD2 morphants.
2013-11-12 | GSE47578 | GEO
Project description:During Xenopus gastrulation, dorsal stabilization of β-Catenin at the earliest stage and subsequent target genes expression are critical for dorsal-ventral axis determination. However, many β-Catenin targets that mediate this process are still unkown. Here through RNA-seq analysis of β-Catenin knockdown embryos and self-regulating dorsal and ventral half embryos at early gastrula, we define an early β-Catenin gene signature that is downregulated by β-Catenin MO and enriched in dorsal gastrula tissues. This gene signature includes classic Spemann organizer genes, as well as other novel genes. Further analyses revealed that the early β-Catenin gene signature is positively correlated with LiCl treated, Wnt8 and Siamois mRNA-induced genes, consistent with their early role in dorsal-ventral axis formation. Our results also show that St 10.5 is the appropriate stage to uncover β-Catenin target genes that regulate dorsal-ventral patterning than St 9. Meanwhile, the multi-growth factor antagonist Cerberus inhibits part of the early β-Catenin gene signature and also controls the expression of a unique set of genes. Our findings provide new insight into the pivotal role of β-catenin in dorsal-ventral axis determination and can serve a fruitful resource for this field.
2017-03-15 | GSE93195 | GEO
Project description:Regional gene expression in the Xenopus gastrula
| PRJNA102459 | ENA
Project description:To identify genes with different expression levels in Xenopus laevis embryos of different sizes, RNAseq of middle gastrula RNA of the wild-size and artificially prepared half-size embryos was done. As a result, several genes with drastically different expression between these two types of embryos were found.
2020-09-29 | GSE158664 | GEO