Sponge metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA297395 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We deep sequence DNA associated with immunoprecipitated chromatin containing histones with specific post-translational modifications (PTMs) to identify transcriptionally active or repressed regions of the genome of the sponge Amphimedon queenslandica.
2017-03-31 | GSE79645 | GEO
Project description:Transcriptomic data for 59 single embryos and larvae samples of the sponge Amphimedon queenslandica Transcriptomic data for 59 single embryos and larvae samples of the sponge Amphimedon queenslandica
2014-01-24 | E-GEOD-54364 | biostudies-arrayexpress
Project description:Transcriptomic data for 59 single embryos and larvae samples of the sponge Amphimedon queenslandica
2014-01-24 | GSE54364 | GEO
Project description:Vertebrates have highly methylated genomes at CpG positions while most invertebrates have sparsely methylated genomes. Therefore, hypermethylation is considered a major innovation that shaped the genome and the regulatory roles of DNA methylation in vertebrates. However, here we report that the marine sponge Amphimedon queenslandica, belonging to one of the earliest branching animal lineages, has evolved a hypermethylated genome with remarkable similarities to that of a vertebrate. Despite major differences in genome size and architecture, independent acquisition of hypermethylation reveal common distribution patterns and repercussions for genome regulation between both lineages. Genome wide depletion of CpGs is counterbalanced by CpG enrichment at unmethylated promoters, mirroring CpG islands. Furthermore, a subset of CpG-bearing transcription factor motifs are enriched at Amphimedon unmethylated promoters. We find that the animal-specific transcription factor NRF has conserved methyl-sensitivity over 700 million years, indicating an ancient cross-talk between transcription factors and DNA methylation. Finally, the sponge shows vertebrate-like levels of 5-hydroxymethylcytosine, the oxidative derivative of cytosine methylation involved in active demethylation. Hydroxymethylation is concentrated in regions that are enriched for transcription factor motifs and show developmentally dynamic demethylation. Together, these findings push back the links between DNA methylation and its regulatory roles to the early steps of animal evolution. Thus, the Amphimedon methylome challenges the prior hypotheses about the origins of vertebrate genome hypermethylation and its implications for regulatory complexity.
2019-08-02 | GSE124016 | GEO
Project description:To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors (TFs) bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs, the evolution of enhancers has been difficult to trace because of their fast evolution. Here, we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed, three were located in conserved syntenic gene regions that are unique to animals (Islet–Scaper, Ccne1–Uri, Tdrd3–Diaph3). Despite diverging over 700 million years ago and a dearth of sequence identity, sponge enhancers are able to drive cell type-specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse, which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.
2019-11-30 | E-MTAB-7846 | biostudies-arrayexpress
Project description:We performed single-cell transcriptome analysis (using MARS-seq) in the sponge Amphimedon queenslandica (adult and larval stages), in the ctenophore Mnemiopsis leidyi (adult stage), and in the placozoan Trichoplax adhaerens (adult stage). Additionally we performed bulk iChIP experiments (2 replicates of each experiment) using antibodies against H3K4me3 and H3K4me2 in adult Mnemiopsis leidyi and adult Trichoplax adhaerens.
2018-07-05 | GSE111068 | GEO
Project description:To assess how larvae of different ages vary in their responses to different settlement cues, we induced individual Amphimedon queenslandica larvae with one of three different settlement cues at 1.5, 3, 5, and 8 hours post emergence (hpe) from the adult sponge. The settlement cues were (1) the articulated coralline algae Amphiroa fragilissima, (2) the crustose coralline algae Mesophyllum sp., and (3) the filtered seawater (FSW) negative control. We used CEL-Seq2, an RNA-Sequencing approach (Hashimshony et al., 2016), to generate transcriptome data for a total of 144 individuals (larvae and settled post-larvae) at 2 hours post induction (hpi) to the different settlement cues.
2024-06-11 | GSE134077 | GEO
Project description:Poriferans, like the demosponge Amphimedon queenslandica, are the earliest diverging metazoans and may hold the key to understanding the evolution of metazoan pathways. A. queenslandica exhibits a biphasic lifecycle, with free-swimming larvae and sessile adult stages. To study changes in the transcriptome during this period of morphological and ecological transition, we generated poly(A) fragment libraries for A. queenslandica at four developmental stages: precompetent and competent larvae, postlarvae, and adult. These libraries were sequenced using Applied Biosystems SOLiD technology. This study provides the most comprehensive analysis to date of gene expression in the sponge. It has elucidated the genes that define the two main phases of the sponge lifestyle and identified genes that are important for competence and metamorphosis. More importantly, this study has provided insights into the expression of the genes that characterize metazoan features, such as cell adhesion and differentiation, in an early metazoan. 4 stages sequenced: precompetent larvae, competent larvae, postlarvae, adult
2012-07-10 | E-GEOD-29978 | biostudies-arrayexpress
Project description:To determine the optimal RNA-Seq approach for animal host-bacterial symbiont analysis, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont, for which genomes of the animal host and three most abundant bacterial symbionts are available.
2022-06-06 | GSE205425 | GEO
Project description:Poriferans, like the demosponge Amphimedon queenslandica, are the earliest diverging metazoans and may hold the key to understanding the evolution of metazoan pathways. A. queenslandica exhibits a biphasic lifecycle, with free-swimming larvae and sessile adult stages. To study changes in the transcriptome during this period of morphological and ecological transition, we generated poly(A) fragment libraries for A. queenslandica at four developmental stages: precompetent and competent larvae, postlarvae, and adult. These libraries were sequenced using Applied Biosystems SOLiD technology. This study provides the most comprehensive analysis to date of gene expression in the sponge. It has elucidated the genes that define the two main phases of the sponge lifestyle and identified genes that are important for competence and metamorphosis. More importantly, this study has provided insights into the expression of the genes that characterize metazoan features, such as cell adhesion and differentiation, in an early metazoan.
2012-07-10 | GSE29978 | GEO