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Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity

ABSTRACT: 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.

ORGANISM(S): Amphimedon queenslandica

PROVIDER: GSE79645 | GEO | 2017/03/31

SECONDARY ACCESSION(S): PRJNA316591

REPOSITORIES: GEO

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A high-resolution Amphimedon queenslandica transriptomic timecourse

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

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Project description:Metagenome from the sponge Amphimedon queenslandica

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A high-resolution Amphimedon queenslandica transriptomic timecourse

Project description:Transcriptomic data for 59 single embryos and larvae samples of the sponge Amphimedon queenslandica

2014-01-24 | GSE54364 | GEO

RNA-seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers

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

Convergent evolution of a vertebrate-like methylome in a marine sponge

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

Early metazoan cell type diversity and the evolution of multicellular gene regulation

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

Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity.

Project description:Combinatorial patterns of histone modifications regulate developmental and cell type-specific gene expression and underpin animal complexity, but it is unclear when this regulatory system evolved. By analysing histone modifications in a morphologically-simple, early branching animal, the sponge Amphimedonqueenslandica, we show that the regulatory landscape used by complex bilaterians was already in place at the dawn of animal multicellularity. This includes distal enhancers, repressive chromatin and transcriptional units marked by H3K4me3 that vary with levels of developmental regulation. Strikingly, Amphimedon enhancers are enriched in metazoan-specific microsyntenic units, suggesting that their genomic location is extremely ancient and likely to place constraints on the evolution of surrounding genes. These results suggest that the regulatory foundation for spatiotemporal gene expression evolved prior to the divergence of sponges and eumetazoans, and was necessary for the evolution of animal multicellularity.

| S-EPMC5429095 | biostudies-literature

Transcriptomes of individual Amphimedon queenslandica larvae and settled post-larvae that were presented with one of three different settlement cues at different times (hours) post emergence from the adult sponge

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

Transcriptome of the demosponge Amphimedon queenslandica at life cycle transitions

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

Ribosomal RNA-depletion provides an efficient method for successful dual RNA-Seq expression profiling of a marine sponge holobiont

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

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