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[E-TABM-722] Transcription factor binding evolution in five vertebrates

ABSTRACT: [E-TABM-722] Transcription factor binding evolution in five vertebrates

OTHER RELATED OMICS DATASETS IN: GSE22078

PROVIDER: PRJNA128961 | ENA |

REPOSITORIES: ENA

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[E-TABM-722] Transcription factor binding evolution in five vertebrates

Project description:Five-vertebrate ChIP-seq reveals the evolutionary dynamics of trancription factor binding. The SRF files for this experiment can be found in the European Read Archive with study accession number ERP000054. ArrayExpress Submission Date: Apr 07 2010 ArrayExpress Release Date: Apr 08 2010 Publication Author List: Dominic Schmidt; Michael D Wilson; Benoit Ballester; Petra C Schwalie; Gordon D Brown; Aileen Marshall; Claudia Kutter; Stephen Watt; Celia P Martinez-Jimenz; Sarah MacKay; Iannis Talianidis; Paul Flicek; Duncan T Odom Publication Title: Transcription factor binding evolution in five vertebrates Person Roles: submitter Person Last Name: Flicek Person First Name: Paul Person Email: flicek@ebi.ac.uk Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Person Affiliation: EBI

2010-06-02 | GSE22078 | GEO

CEBPA binding in five vertebrates

Project description:CEBPA binding in five vertebrates

| PRJEB2006 | ENA

Transcription Factor binding evolution in five mouse species

Project description:Transcription Factor binding evolution in five mouse species

| PRJEB1247 | ENA

Combinatorial transcription factor binding evolution in five placental mammals

Project description:Combinatorial transcription factor binding evolution in five placental mammals

| PRJEB1571 | ENA

Transcription Factor binding evolution in five mouse species

Project description:This study aims to compar transcription factor binding region between five mouse species.

2013-08-30 | E-MTAB-1414 | biostudies-arrayexpress

The hagfish genome and the evolution of vertebrates

Project description:The hagfish genome and the evolution of vertebrates

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Heart Chamber Evolution Reveals Roles of Gene/Genome Duplications on Continuous Character Evolution in Vertebrates

Project description:We sequenced at mRNA level in adult hearts of zebrafish, pamprey and sea squirt. Combined with other 11 vertebrate heart RNA-Seq data online, we conducted comprehensive evolutionary genomic analyses to address the contribution of gene/genome duplications on heart structure evolution. We observed that number of duplicate genes expressed in heart increased gradually with the increase of heart chamber number along the vertebrate phylogeny, despite that most of them were duplicated at the time near to the origin of vertebrates or more ancient. Our research provides a clear-cut example to show the relationship among gene duplication, continuous character evolution like heart structure evolution and nature selection.

2018-09-28 | GSE73522 | GEO

The hagfish genome and the evolution of vertebrates

Project description:As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a critical window into early vertebrate evolution. Here, we investigate the complex history, timing, and functional role of genome-wide duplications in vertebrates in the light of a chromosome-scale genome of the brown hagfish Eptatretus atami. Using robust chromosome-scale (paralogon-based) phylogenetic methods, we confirm the monophyly of cyclostomes, document an auto-tetraploidization (1RV) that predated the origin of crown group vertebrates ~517 Mya, and establish the timing of subsequent independent duplications in the gnathostome and cyclostome lineages. Some 1RV gene duplications can be linked to key vertebrate innovations, suggesting that this early genomewide event contributed to the emergence of pan-vertebrate features such as neural crest. The hagfish karyotype is derived by numerous fusions relative to the ancestral cyclostome arrangement preserved by lampreys. These genomic changes were accompanied by the loss of genes essential for organ systems (eyes, osteoclast) that are absent in hagfish, accounting in part for the simplification of the hagfish body plan; other gene family expansions account for hagfishes’ capacity to produce slime. Finally, we characterise programmed DNA elimination in somatic cells of hagfish, identifying protein-coding and repetitive elements that are deleted during development. As in lampreys, the elimination of these genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline/pluripotency functions. Reconstruction of the early genomic history of vertebrates provides a framework for further exploration of vertebrate novelties.

2024-01-04 | GSE230176 | GEO

Inducible overexpression of zebrafish microRNA-722 suppresses chemotaxis of human neutrophil like cells

Project description:To assess the effect of miR-722 in mature neutrophil like cells driven by and inducible promoter to avoid affecting neutrophil diffrentiation

2021-09-09 | GSE126527 | GEO

Evolution of Modularity, Interactome and Functions of GIV/Girdin (CCDC88A) from Invertebrates to Vertebrates

Project description:PDZ domains are one of the most abundant protein domains in eukaryotes and frequently found on junction-localized scaffold proteins. Various signaling molecules bind to PDZ proteins via PDZ-binding motifs (PBM) and finetune cellular signaling. Here we describe the presence of a PBM on GIV/Girdin (CCDC88A) that is conserved throughout evolution, from invertebrates to vertebrates, and is generated as a long isoform-variant in humans, which we named GIV-L. Unlike GIV, which lacks PBM and is cytosolic, GIV-L localizes to the cell junctions, and has a unique PDZ-interactome, which impacts GIV-L’s ability to bind and activate trimeric G-protein, Gi through its guanine-nucleotide exchange modulator (GEM) module; the GEM module is found exclusively in vertebrates. Thus, the two functional modules in GIV evolved sequentially: the ability to bind PDZ proteins via the PBM evolved earlier in invertebrates, whereas G-protein binding and activation may have evolved later only among vertebrates. Phenotypic studies in Caco-2 cells revealed that GIV and GIV-L may have antagonistic effects on cell growth, proliferation (cell cycle), and survival. Immunohistochemical analyses in human colon tissues showed that GIV expression increases with a concomitant decrease in GIV-L during cancer initiation. Taken together, these findings reveal how GIV/CCDC88A in humans displays evolutionary flexibility in modularity, which allows the resultant isoforms to play opposing roles either as a tumor suppressor (GIV-L) or as an oncogene (GIV).

2021-09-09 | PXD022601 | Pride

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