Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos

ABSTRACT: Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequencing. By combining bioinformatic analysis of the small RNA-seq dataset with experimental validation, we identify novel microRNAs and Piwi-interacting RNAs. We show that microRNA expression is highly dynamic and spatially localized in early embryos in contrast to Piwi-interacting RNAs, and we validate a novel microRNA prediction pipeline. We go on to identify a new class of small intronic non-coding RNAs, that we name sincRNAs. On a genome-wide scale we find that genes containing sincRNA clusters are transcriptionally repressed. Our data suggest a novel mechanism of sincRNA-mediated gene silencing in vertebrates. Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development.

ORGANISM(S): Xenopus (Silurana) tropicalis

SUBMITTER: Caroline Hill

PROVIDER: E-GEOD-38605 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

Project description:Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryogenesis. Here, we report on the epigenetic and transcriptome genome-wide maps of gastrula-stage Xenopus tropicalis embryos using massive parallel sequencing of cDNA (RNA-seq) and DNA obtained by chromatin immunoprecipitation (ChIP-seq) of histone H3 K4 and K27 trimethylation and RNA Polymerase II (RNAPII). These maps identify promoters and transcribed regions. Strikingly, genomic regions featuring opposing histone modifications are mostly transcribed, reflecting spatially regulated expression rather than bivalency as determined by expression profile analyses, sequential ChIP, and ChIP-seq on dissected embryos. Spatial differences in H3K27me3 deposition are predictive of localized gene expression. Moreover, the appearance of H3K4me3 coincides with zygotic gene activation, whereas H3K27me3 is predominantly deposited upon subsequent spatial restriction or repression of transcriptional regulators. These results reveal a hierarchy in the spatial control of zygotic gene activation. ChIP-seq profiles of two histone modifications (H3K4me3 and H3K27me3) and RNA Polymerase II, and a RNA-seq profile, of gastrula stage Xenopus tropicalis embryos

2009-09-15 | E-GEOD-14025 | biostudies-arrayexpress

Foxh1/nodal defines context-specific direct maternal Wnt/Beta-catenin target gene regulation in early development

Project description:This study aimed to further understand context-specific direct Wnt target gene expression through the use of beta-catenin and FoxH1 ChIP Sequencing data at various developmental stages representing both maternal and zygotic Wnt signalling. Results were further supported through the use of RNA sequencing data from beta-catenin, FoxH1 and nodal gene knock down assays.

2020-06-21 | E-MTAB-8555 | biostudies-arrayexpress

In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency

Project description:Brachyury (Xbra/Xbra3) knock-down embryos of the frog Xenopus tropicalis were profiled to quantify neuro-mesodermal cell fate switches at a transcriptional level. Transcriptional profiling of Xbra/Xbra3 double morphants at early tadpole stage (RNA-Seq) in biological triplicates.

2013-09-19 | E-GEOD-48663 | biostudies-arrayexpress

In vivo T-box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuro-mesodermal Bipotency.

Project description:We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesodermal stem cells and determine their bipotential fates in the Xenopus tropicalis frog embryo. Binding profiles for Xbra, Eomes and VegT in X. tropicalis embryos (ChIP-Seq)

2013-09-19 | E-GEOD-48560 | biostudies-arrayexpress

Polycomb Protein Ezh1 Promotes RNA Polymerase II Elongation

Project description:Polycomb group (PcG) proteins initiate the formation of repressed chromatin domains and regulate developmental gene expression. A mammalian PcG protein, Enhancer of Zeste homolog 2 (Ezh2), triggers transcriptional repression by catalyzing the addition of methyl groups onto lysine-27 of histone H3 (H3K27me2/3)1. This action facilitates the binding of other PcG proteins to histone H3 and compaction of chromatin. Interestingly, there exists a paralog of Ezh2, termed Ezh1, whose primary function remains unclear. Here, we provide evidence for genome-wide association of Ezh1 with active epigenetic marks, RNA polymerase II (PolII) and mRNA production. Ezh1 depletion reduced global PolII occupancy within gene bodies and resulted in delayed transcriptional activation during differentiation of skeletal muscle cells. Conversely, ectopic expression of wild-type Ezh1 led to premature gene activation and rescued PolII-elongation defects in Ezh1-depleted cells. Collectively, these findings reveal an unanticipated role of a PcG protein in promoting mRNA transcription. Examination of 3 different histone modifications, 3 modified forms of RNA polymerase II, Ezh1, Ezh2 and mRNA levels in a skeletal muscle cells at various developmental stages.

2011-11-23 | E-GEOD-25549 | biostudies-arrayexpress

Nucleotide composition-linked divergence of vertebrate core promoter architecture

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

Identification and quantification of allele specific proteins and homeolog expression bias in an allopolyploid non-model crop by integrating transcriptomics and proteomics.

Project description:The fate of doubled genes, from allopolyploid or autopolyploid origin, is controlled at multiple levels within the central dogma: gene loss or silencing, neo- and/or sub functionalization, inter genomic transfer, allele dominance/co-dominance, differences in transcription/translation efficiency, post translational modifications… These regulatory processes through evolution have caused a plethora of genotype x environment interactions displayed in the modern day phenotypes. The study of non-model crops is challenging but solutions are emerging. More and more, one gets insight into the tolerance mechanisms of a specific genotype. By integrating transcriptomics into our proteomic data, we studied the genetic diversity of an allopolyploid ABB banana, a tolerant genotype, and compared it to two different sensitive AAA genotypes. The root growth of the ABB cultivar was 60 % higher under mild osmotic stress. 234,000 spectra were aligned and quantified, resulting in 2,753 identified root proteins. 383 gene loci displayed genotype specific differential expression whereof 252 showed at least one Single Amino Acid Polymorphism (SAAP). The homeoallelic contribution was assessed using transcriptome read alignment, thus revealing each allele contribution at the RNA level. This provides insight in the structure and the organization of the triploid genome. In the ABB cultivar, allele expressions are supposed to follow a 1/3 and 2/3 pattern. We found that many genes deviated from this expectation and we show that 32 gene loci even displayed a 100% read preference for the allele that was unique for the ABB tolerant genotype , suggesting that the presence of unique alleles and homoelog expression bias is correlated to the observed phenotype.

2018-01-29 | PXD006375 | Pride

Principles of nucleation of H3K27 methylation during embryonic development

Project description:During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 K27 trimethylation (H3K27me3). However, the developmental origins of this regulation are unknown. Here, we report on H3K27me3 deposition dynamics in Xenopus embryos, on sequence elements that initiate deposition during pluripotency, and the sequence characteristics that segregate Polycomb-regulated domains from the rest of the genome. Strikingly, although PRC2 binds widely to active enhancers, H3K27me3 is only deposited at a small subset of these sites. Using a Support Vector Machine algorithm these sequences can be predicted accurately on basis of DNA sequence alone, with a sequence signature conserved between humans, frog and fish. The results suggest a genetic-default model in which genomic sequence constrains Polycomb regulation. ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development

2013-11-28 | E-GEOD-41161 | biostudies-arrayexpress

Proteogenomics of Candida tropicalis – an opportunistic pathogen

Project description:Candida tropicalis is an opportunistic pathogen which causes candidiasis in immune-compromised individuals. It is one of the members of the non-albicans group of Candida that are known to be azole resistant and is frequently seen in individuals being treated for cancers, HIV-infection and bone-marrow transplant. Although the genome of C. tropicalis was sequenced in the year 2009, the genome annotation has not been supported by experimental validation. In the present study, we have carried out in-depth proteomic profiling of C. tropicalis using high-resolution Fourier transform mass spectrometry and mapped ~44% of the computationally predicted protein-coding genes with peptide level evidence. In addition to identifying 2,740 proteins in the cell lysate of this yeast, we also analysed the proteome of the conditioned media of C. tropicalis culture and identified several unique secreted proteins among a total of 780 proteins. By subjecting the mass spectrometry data derived from cell lysate and conditioned media to proteogenomic analysis, we identified 86 novel genes, 12 novel exons and corrected 49 computationally predicted gene models. To our knowledge, this is the first high-throughput proteomic study to refine the genome annotation of C. tropicalis.

2017-05-08 | PXD001071 | Pride

Transcriptional Profiling of Psoriasis Using RNA-seq Reveals Previously Unidentified Differentially Expressed genes

Project description:The transcriptomic profiling of psoriasis has led to an increased understanding of disease pathogenesis. Although microarray technologies have been instrumental in this regard, it is clear that these tools detect an incomplete set of DEGs. RNA-seq can be used to supplement these prior technologies. Here, the use of RNAseq methods substantially increased the number of psoriasis-related DEGs. Furthermore, DEGs that were uniquely identified by RNA-seq, but not in other published microarray studies, further supported the role of IL-17 and tumor necrosis factor-a synergy in psoriasis. Examination of one of these factors at the protein level confirmed that RNA-seq is a powerful tool that can be used to identify molecular factors present in psoriasis lesions, and may be useful in the identification of therapeutic targets that to our knowledge have not been reported previously. Further studies are in progress to determine the biological significance of DEGs uniquely discovered by RNA-seq. To define the transcriptomic profile of psoriatic skin, three pairs of lesional and nonlesional skin biopsy specimens were taken from patients with untreated moderate-to-severe plaque psoriasis.

2012-10-22 | E-GEOD-41745 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data