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ATAC and Mediator coactivators form a stable complex and regulates a set of non-coding RNA genes

ABSTRACT: The ATAC histone acetyl-transferase (HAT) and the Mediator coactivator complexes regulate independent and distinct steps during transcription initiation and elongation. Here we report the identification of a new stable molecular assembly formed between the ATAC and the Mediator complex in mouse embryonic stem cells. Moreover, we identify LUZP1 as a subunit of this meta coactivator complex (MECO). Finally, we demonstrate that MECO regulates a subset of RNA polymerase II transcribed non-coding RNA genes. Our findings establish that transcription coactivator complexes can form stable sub-complexes in order to facilitate their combined actions on specific target genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE21717 | GEO | 2010/06/25

SECONDARY ACCESSION(S): PRJNA127145

REPOSITORIES: GEO

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ATAC and Mediator coactivators form a stable complex and regulates a set of non-coding RNA genes

Project description:The ATAC histone acetyl-transferase (HAT) and the Mediator coactivator complexes regulate independent and distinct steps during transcription initiation and elongation. Here we report the identification of a new stable molecular assembly formed between the ATAC and the Mediator complex in mouse embryonic stem cells. Moreover, we identify LUZP1 as a subunit of this meta coactivator complex (MECO). Finally, we demonstrate that MECO regulates a subset of RNA polymerase II transcribed non-coding RNA genes. Our findings establish that transcription coactivator complexes can form stable sub-complexes in order to facilitate their combined actions on specific target genes. For ChIP-seq analysis, 300µg of chromatin (DNA) was incubated with GST (mock), LUZP1 and GCN5 antibodies. Retrieved purified DNA was sequenced using Illumina Genome Analyzer II following manufacturer recommendations. Illumina raw files were aligned against reference (mouse mm9) genome using the eland program allowing one mismatch. Enrichment clusters were detected using MACS (Zhang et al., 2008). The retrieved peaks were filtered (max size 1000bp, min size 100bp) and repeat masked, to establish the final binding sites lists. Peaks were annotated using the GPAT web server (Krebs et al., 2008) using ENSEMBL gene 57 database.

2010-06-24 | E-GEOD-21717 | biostudies-arrayexpress

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

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

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

2011-11-05 | GSE31052 | GEO

Mediator and Pol II form diffraction-sized condensates dependent on active transcription in living stem cells

Project description:Gene activation is thought to involve a multistep process whereby transcription factors bind to distal enhancer sites and recruit the Mediator complex which contacts the pre-initiating RNA Polymerase II (Pol II) complex assembled at the start site of the gene. The interaction of Mediator and Pol II has yet to be observed in the nucleus of living cells and the dynamics of this interaction are not yet elucidated. Here we use quantitative live cell super-resolution and light sheet imaging to study the organization and dynamics of endogenous Mediator and Pol II directly in living mouse embryonic stem cells. In addition to forming transient clusters with average lifetimes of 11.1 (± 0.9) s, and 12.1 (± 1.4) s respectively, Mediator and Pol II also form large and stable clusters in stem cells (~15 stable clusters per cell). The large and stable Mediator and Pol II clusters gradually disappear within hours after induction of stem cell differentiation. Mediator and Pol II colocalize in the large clusters. Inhibition of Brd4 bromodomains necessary for enhancer association eliminates both Mediator and Pol II stable clusters, and inhibition of transcription elongation selectively eliminates stable Pol II but not stable Mediator clusters. Tracking of Mediator and Pol II stable clusters suggests they are chromatin associated and they coalesce upon contact, a property associated with phase separated droplets. We conclude that Mediator and Pol II associate in diffraction-sized condensates with a defined lifetime dependent on active transcription in living stem cells.

2018-07-22 | GSE115436 | GEO

MEDIATOR subunit med8 binding in Saccharomyces cerevisiae

Project description:The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator – histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis, that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. Med8-TAP strain ChIPed with IgG beads vs. Input in Saccharomyces cerevisiae

2011-11-22 | E-GEOD-28613 | biostudies-arrayexpress

Distinct patterns of histone acetyltransferase and Mediator deployment at yeast protein-coding genes

Project description:The transcriptional co-activators Mediator and two histone acetyltransferase (HAT) complexes, NuA4 and SAGA, play global roles in transcriptional activation. Here we explore the relative contributions of these factors to RNA polymerase II association at specific genes and gene classes by rapid nuclear depletion of key complex subunits. We show that the NuA4 HAT Esa1 differentially affects certain groups of genes, whereas the SAGA HAT Gcn5 has a weaker but more uniform effect. Relative dependence on Esa1 and Tra1, a shared component of NuA4 and SAGA, distinguishes two large groups of co-regulated growth-promoting genes. In contrast, we show that the activity of Mediator is particularly important at a separate, small set of highly transcribed TATA box-containing genes. Our analysis indicates that at least three distinct combinations of co-activator deployment are used to generate moderate or high transcription levels, and suggests that each may be associated with distinct forms of regulation.

2018-08-15 | GSE109235 | GEO

H3K9ac ChIP-seq in WT, SAGA and ATAC mutant mouse embryonic stem cells

Project description:Assess H3K9ac levels in WT and mutant ES E14 strains using ChIP-seq. Mutant strains are depleted for subunits of the coactivator complexes SAGA (Supt7l KO) or ATAC (AID-Yeats2) or of HAT subunits (AID-Tada3, Tada2a+Tada2b KO) using constitutive knock-out (KO) or the auxin-inducible degron (AID) system.

2021-08-03 | GSE175903 | GEO

MEDIATOR subunit med8 binding in Saccharomyces cerevisiae

2011-11-22 | GSE28613 | GEO

Transcriptional noise, gene activation, and roles of SAGA and Mediator Tail measured using nucleotide recoding single cell RNA-seq

Project description:The populational variance of eukaryotic transcription differs by gene, and can be range from constitutive to bursty in nature. Exemplary bursty yeast genes tend to rely on SAGA and Mediator Tail (coactivator-redundant, CR) for transcription, and often contain TATA boxes in their promoters. To dissect gene-specific transcriptional bursting and the roles of coactivator complexes in regulating bursting in yeast, we performed genome-wide nascent single-cell RNA-seq. Examining the transcriptional variance-mean relationship (Fano factor) for thousands of yeast genes across cell populations, we found that CR-class genes generally display burstier transcription than TFIID-class genes, regardless of expression level. We also found that the cell cycle-dependent activation of yeast histone genes correlates with an increase in Fano. Finally, we assessed the consequences of rapid depletion of SAGA or Mediator Tail coactivator complex subunits. On a per-gene basis, we observed a strong relationship between bulk transcriptional fold change and the change in fraction of yeast cells actively transcribing (Fon), and a weak relationship between bulk transcriptional fold change and the change in mean expression per cell (MPC). We also observe gene-specific variation in Fon, MPC, and Fano following coactivator depletion. These results provide insight into gene-specific transcriptional kinetics and the roles of coactivator complexes in gene activation and transcriptional bursting.

2024-06-02 | GSE247795 | GEO

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