Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates
Ontology highlight
ABSTRACT:
ORGANISM(S): Xenopus tropicalis
PROVIDER: GSE145619 | GEO | 2020/12/18
REPOSITORIES: GEO
Similar Datasets
Project description:In this study, we have addressed the involvement of chromatin organizer SATB2 in orchestrating zygotic genome activation and neural crest specification during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Comparative analysis with mouse embryos highlighted conserved molecular mechansisms for Satb2 during neural crest specification.
2021-09-02 | GSE183002 | GEO
Project description: Not available
| S-EPMC8090851 | biostudies-literature
Project description:Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates
| PRJNA607864 | ENA
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:Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated prior to biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from over 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas. 3 replicates from GM12878 and HL-60 cell lines collected for differential gene expression analysis.
2015-05-07 | E-GEOD-68102 | biostudies-arrayexpress
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:A genome decoded chordate Ciona intestinalis is one of the suitable animal for analyzing genetic controls in early embryogenesis and zygotically expressed genes are especially intensely studied. However maternally expressed genes are less studied than zygotic ones because of their huge numbers. These microarray experiments were carried out to screen rapidly degrading mRNA to identify crucial maternal mRNAs for Ciona embryogenesis in relatively a short period before their degradation. Two samples (unfertilized eggs vs 32-cell stage embryos), two biological replicates, dye Swap design
2010-12-04 | E-GEOD-25817 | biostudies-arrayexpress
Project description:The vertebrate body plan is established through inductive signaling during gastrulation via a signaling center, which is called the Spemann-Mangold organizer (SMO) in the developmental model Xenopus laevis, the South African Clawed Frog. Here, we performed a multiplexed quantitative proteomic screen of the SMO in contrast with the rest of the embryo (RE). Wild-type embryos were cultured to the 32-cell stage, where precursor cells of the SMO were injected with a fluorescent lineage tracing dye. These experimental embryos were cultured to stage 10 (beginning of gastrulation), whence the fluorescently labelled cells were dissected. The proteome of the SMO and the RE were quantified using multiplexing quantification. The tissue samples were processed using a bottom-up proteomic workflow and analyzed using LC-MS3. The resulting data revealed an upregulation of oxidative phosphorylation (OXPHOS) in the SMO tissues.
2024-01-10 | PXD043583 | Pride
Project description:In many organisms, early embryonic development is driven by maternally provided transcription factors until the controlled onset of transcription during zygotic genome activation (ZGA). The regulation of chromatin accessibility and its relationship to gene activity during this transition remains poorly understood. Here, we generated chromatin accessibility maps for the early stages of zebrafish development spanning genome activation and the onset of lineage specification. We find that during this period, chromatin accessibility increases at regulatory elements. This is independent of RNA pol II-mediated transcription, with the exception of the miR-430 locus. Instead, accessibility often precedes the transcription of associated genes. Loss of the maternal transcription factors pou5f3, sox19b, and nanog, which are known to be required for zebrafish ZGA, results in decreased accessibility at regulatory elements. Finally, we show that accessibility of regulatory regions, especially when established by Pou5f3, Sox19b and Nanog, is predictive for future transcription. Together, our results suggest that maternally provided transcription factors prime genes for activity during zygotic genome activation.
2020-01-08 | GSE130944 | GEO
Project description:The first embryonic cell divisions rely on maternally stored mRNA and proteins. The zygotic genome is initially transcriptionally silenced and activated later in a process called zygotic genome activation (ZGA). ZGA in any species is still a poorly understood process; the timing of transcription onset is controversial and the identity of the first transcribed genes unclear. Zebrafish, Danio rerio, is a rapidly developing vertebrate model, which is accessible to experimentation and global studies before, during and after ZGA. To accurately determine the onset of ZGA and to identify the first transcripts in zebrafish, we developed a metabolic labeling method, utilizing the ribonucleotide analog 4-thio-UTP, which allows efficient and specific affinity purification of newly transcribed RNA. Using deep sequencing, we characterized the onset of transcription in zebrafish embryos at 128-, 256-, and 512-cell stages. We identified 592 nuclear-encoded zygotically transcribed genes, comprising 670 transcript isoforms. Mitochondrial genomes were highly transcribed at all time points. Further, bioinformatic analysis revealed an enrichment of transcription factors and miRNAs among the newly transcribed genes, suggesting mechanistic roles for the early genes that are required to activate subsequent gene expression programs in development. Interestingly, analysis of gene-architecture revealed that zygotically transcribed genes are often intronless and short, reducing transcription and processing time of the transcript. The newly generated dataset enabled us to compare zygotically transcribed genes over a broad phylogenetic distance with fly and mouse early zygotic genes. This analysis revealed that short gene length is a common characteristic for early zygotically expressed genes. However, we detected a poor level of overlap for shared orthologs.
2014-01-16 | E-GEOD-47709 | biostudies-arrayexpress