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

ABSTRACT: Assess chromatin accessibility in WT and mutant ES E14 strains using ATAC-seq. Mutant strains are depleted for subunits of the coactivator complexes SAGA (Supt7l KO) or ATAC (Yeats2, Zzz3) using constitutive knock-out (KO) or the auxin-inducible degron (AID) system.

ORGANISM(S): Mus musculus

PROVIDER: GSE175902 | GEO | 2021/08/03

REPOSITORIES: GEO

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

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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.

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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.

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

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

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The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma [ATAC-Seq]

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The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation

Project description:Recognition of post-translational modifications on histones by epigenetic readers is a fundamental mechanism for the regulation of chromatin and transcription. Compared to the large number of readers that recognize histone methylation, only a few acetyllysine readers have been identified, including bromodomain, YEATS, and double plant homeodomain zinc finger (DPF). Here, we report the identification of a novel reader of histone H3, the ZZ-type zinc finger (ZZ) domain of ZZZ3, a subunit of the Ada-Two-A Containing (ATAC) histone acetyltransferase complex. The solution NMR structure of the ZZ in complex with the H3 peptide reveals a unique histone-binding mechanism involving caging of the N-terminal Alanine 1 of histone H3 in an acidic cavity of the ZZ domain. Importantly, acetylation on Lysine 4 of H3 (H3K4ac) enhances the binding, and in cells, ZZZ3 colocalizes with H3K4ac across the genome. The recognition of histone acetylation by ZZ is essential for chromatin occupancy of ZZZ3 and functions of the ATAC complex. Depletion of ZZZ3 or disruption of the ZZ-H3 interaction dampens ATAC dependent promoter histone H3K9 acetylation and the expression of ribosomal protein encoding genes. Overall, our study identifies the ZZ domain of ZZZ3 as a novel epigenetic reader that links the GCN5/ATAC complex to histone acetylation.

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