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The ATAC epigenomic profiling of Capitella teleta development

ABSTRACT: Capitella teleta is a model specie in marine annelids research, to gain insight into its development, we performed time-course ATAC-seq ranging from 64 cell to stage 8 larvae, to profiling the gene regulation dynamics

ORGANISM(S): Capitella teleta

PROVIDER: GSE210814 | GEO | 2022/11/16

REPOSITORIES: GEO

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The developmental transcriptome profiling of Capitella teleta

Project description:Capitella teleta is a model specie in marine annelids research, to gain insight into its development, we performed time-course RNA-seq ranging from 64 cell to stage 7 larvae, to profiling the gene expression dynamics

2022-11-16 | GSE192478 | GEO

The developmental transcriptome and epigenome of Owenia fusiformis reveal the development and evolution of mitraria larvae

Project description:Owenia fusiformis has a unique mitraria larvae form which is different to other marine spiralians. we utilize RNA-seq and ATAC-seq to profile the gene expression and chromatin accessibility to understand their development and evolution.

2022-05-04 | GSE184126 | GEO

The developmental transcriptome and epigenome of Owenia fusiformis reveal the development and evolution of mitraria larvae [dataset2]

2022-11-16 | GSE202283 | GEO

Project description:SAGA and ATAC are two related transcriptional coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development but the precise role of the two complexes in RNA polymerase II transcription in mammals is less understood. To determine whether SAGA and ATAC have redundant or specific functions dependent on their HAT activities, we compared the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC subunits are required for complex assembly, mouse ESC growth and self-renewal. Additionally, ATAC, but not SAGA subunits are required for ESC viability by regulating the transcription of translation-related genes. Surprisingly, depletion of specific or shared HAT module subunits caused a global decrease in histone H3K9 acetylation, but did not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for viability and self-renewal of mouse ESCs by regulating transcription through different pathways, in a HAT-independent manner.

2021-08-11 | PXD027026 | Pride

The adult tissue transcriptome of Owenia fusiformis

Project description:Owenia fusiformis is an ancestral sister group to the annelids, it has a unique "head larvae" type named mitraria larvae. To identify the gene expressed in different tissues, especially the gene expressed in head region, we dissected the 5 female worms and 1 male worm to get 9 different tissues, and extracted their RNA. The sequencing were performed on BGISEQ-500 platform, and the mapping were done with Kallisto and normalization was performed with DEseq2.

2022-11-16 | GSE210813 | GEO

The ATAC and SAGA coactivator complexes assemble co-translationally, but their cellular localization properties and functions are distinct

Project description:To understand the precise mechanism that guide the formation of multisubunit complexes is of key importance. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here we demonstrate that the distinct modules of ATAC (ADA Two A Containing) and SAGA (SPT ADA GCN5 Acetyltransferase), two lysine acetyl transferase-containing transcription coactivator complexes, assemble co-translationally in the cytoplasm of mammalian cells. Fully assembled SAGA complex forms in the cytoplasm of mammalian cells and cytoplasmic SAGA acetylates non-histones proteins, before imported in the nucleus. In contrast, ATAC has no cytoplasmic functions as it cannot be detected in the cytoplasm of mammalian cells. However, fully assembled endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related co-activators, ATAC and SAGA, assemble by using co-translational pathways, but their subcellular localization, cytoplasmic detectability and functions are distinct.

2023-09-27 | PXD038695 | Pride

ATAC

Project description:ATAC

| PRJEB46363 | ENA

Bulk ATAC-seq of primate cerebral organoids

Project description:Bulk ATAC-seq was performed on human, chimpanzee, bonobo, and macaque stem cell-derived cerebral organoids. ATAC-seq was performed on day 60 (2 months old) and day 120 (4 months old) cerebral organoids.

2019-10-16 | E-MTAB-8228 | biostudies-arrayexpress

Chordoma ATAC-Seq

Project description:Chromatin profiling of chordoma collected by the Broad chordoma target discovery project paired end ATAC-Seq profiling in the UCH2 and MUGCHOR chordoma cell lines

2015-07-11 | E-GEOD-70771 | biostudies-arrayexpress

SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers

Project description:Metazoan SAGA and ATAC are distinct multi-subunits complexes that share the same catalytic HAT subunit (GCN5 or PCAF). Here we show that these human HAT complexes are targeted to different genomic loci representing functionally distinct regulatory elements both at broadly expressed and tissue specific genes. While SAGA can principally be found at promoters, ATAC is recruited to promoters and enhancers, yet only its enhancer binding is cell-type specific. Furthermore, we show that ATAC functions at a set of enhancers that are not bound by p300, revealing a new class of enhancers not yet identified. These findings demonstrate important functional differences between SAGA and ATAC coactivator complexes at the level of the genome and define a novel role for the ATAC complex in the regulation of a set of enhancers. Examination of SPT20 in two different cell types.

2011-11-05 | E-GEOD-31052 | biostudies-arrayexpress

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