Xenopus tropicalis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA126041 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists, however for most of these motifs the distribution across species is unknown. Here we report on the comparison of human and amphibian promoter sequences. We have used oligo-capping in combination with deep sequencing to determine transcription start sites in Xenopus tropicalis. To systematically predict regulatory elements we have developed a de novo motif finding pipeline using an ensemble of computational tools. A comprehensive comparison of human and amphibian promoter sequences revealed both similarities and differences in core promoter architecture. Some of the differences stem from a highly divergent nucleotide composition of Xenopus and human promoters. Whereas the distribution of some core promoter motifs is conserved independent of species-specific nucleotide bias, the frequency of another class of motifs correlates with the single nucleotide frequencies. This class includes the well-known TATA box and SP1 motifs, which are more abundant in Xenopus and human promoters, respectively. While these motifs are enriched above the local nucleotide background in both organisms, their frequency varies in step with this background. These differences are likely adaptive as these motifs can recruit TFIID to either CpG island or sharply initiating promoters. Our results highlight both conserved and diverged aspects of vertebrate transcription, most notably showing co-opted motif usage to recruit the transcriptional machinery to promoters with diverging nucleotide composition. This shows how sweeping changes in nucleotide composition are compatible with highly conserved mechanisms of transcription initiation. ChIP-seq profiles of TBP in Xenopus tropicalis stage 12 embryos and TSS-seq profiles of Xenopus oocytes and stage 12 embryos
2010-12-30 | E-GEOD-21482 | biostudies-arrayexpress
Project description:Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists, however for most of these motifs the distribution across species is unknown. Here we report on the comparison of human and amphibian promoter sequences. We have used oligo-capping in combination with deep sequencing to determine transcription start sites in Xenopus tropicalis. To systematically predict regulatory elements we have developed a de novo motif finding pipeline using an ensemble of computational tools. A comprehensive comparison of human and amphibian promoter sequences revealed both similarities and differences in core promoter architecture. Some of the differences stem from a highly divergent nucleotide composition of Xenopus and human promoters. Whereas the distribution of some core promoter motifs is conserved independent of species-specific nucleotide bias, the frequency of another class of motifs correlates with the single nucleotide frequencies. This class includes the well-known TATA box and SP1 motifs, which are more abundant in Xenopus and human promoters, respectively. While these motifs are enriched above the local nucleotide background in both organisms, their frequency varies in step with this background. These differences are likely adaptive as these motifs can recruit TFIID to either CpG island or sharply initiating promoters. Our results highlight both conserved and diverged aspects of vertebrate transcription, most notably showing co-opted motif usage to recruit the transcriptional machinery to promoters with diverging nucleotide composition. This shows how sweeping changes in nucleotide composition are compatible with highly conserved mechanisms of transcription initiation.
2010-12-30 | GSE21482 | GEO
Project description:Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution
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Project description:Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. The most recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. Here we generated epigenetic profiles and determined gene expression in X.laevis embryos to study the consequences of this duplication at the level of the genome, the epigenome, and gene expression.
2017-09-28 | GSE90898 | GEO
Project description:The core-promoter, a stretch of DNA surrounding the transcription-start-site (TSS), is a major integration-point for regulatory-signals controlling gene-transcription. Cellular-differentiation is marked by divergence in transcriptional-repertoire and cell- cycling behaviour between cells of different fates. The role promoter-associated gene- regulatory-networks play in development-associated transitions in cell-cycle- dynamics is poorly understood. This study demonstrates in a vertebrate embryo, how core-promoter variations define transcriptional-output in cells transitioning from a proliferative to cell-lineage specifying phenotype. Assessment of cell-proliferation across zebrafish embryo-development, using the FUCCI-transgenic cell-cycle- phase marker, revealed a spatial and lineage-specific separation in cell-cycling behaviour. To investigate the role differential promoter-usage plays in this process, cap-analysis-of-gene-expression (CAGE) was performed on cells segregated by cycling-dynamics.
2020-06-19 | E-MTAB-8795 | biostudies-arrayexpress
Project description:Retinoid X receptor (RXR) plays an important role in the development of vertebrates, and the agonists of RXR are well-known to induce featured malformations in vertebrate embryos. However, there is no information about the teratogenicity of antagonists of RXR in vertebrate embryos. We exposed embryos of amphibian (Xenopus tropicalis) at stages 10/11 to a highly selective antagonist of RXR (UVI3003).
2014-02-13 | GSE54929 | GEO
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| S-EPMC3098391 | biostudies-literature
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| S-EPMC6396978 | biostudies-literature
Project description:To identify changes in metabolites that correlate with progression of tail regeneration, we collected a timecourse of tissues containing 250 um of tissue anterior to the wound site as well as all regenerating tissue at 0, 3, and 24 hours post amputation. We also collected the posterior 500 um of the developing tail to represent the metabolic profile of uninjured tissues. Tissues from 25 individuals were collected and frozen in more than 5-8 minutes per replicate before processing as in the methods. 104 metabolites were identified in these samples and relative peak intensities were compared to identify changes in abundance corresponding to regeneration. 42 differentially abundant metabolites were found using MetaboAnalyst, the majority of which were increased 24 hours post amputation. Further investigation of these 24 hours post amputation enriched metabolites revealed that these metabolites were largely associated with increased growth and nucleotide metabolism. This finding is in line with the growth of new tissue seen at this timepoint and also suggests that generation of nucleotides are a major factor in sustaining this growth.
2022-08-03 | ST002271 | MetabolomicsWorkbench
Project description: Not available
| S-EPMC8028753 | biostudies-literature