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Super-enhancer driven MYST family histone lysine acetyltransferases are critical for nasopharyngeal carcinoma cell growth and survival

ABSTRACT: Nasopharyngeal carcinoma (NPC) is causally linked to Epstein-Barr virus (EBV) infection, genetic predisposition and environmental factors. Early diagnosis is difficult due to lack of specific symptoms. Many patients have advanced disease at diagnosis and these patients respond to treatment poorly. To better understand the NPC molecular pathogenesis, genome-wide CRISPR screen was used to identify NPC dependency factors. These dependency factors were then linked to their enhancers using H3K27ac HiChIP. The screen identified MYST histone acetyl transferase complex, NF-kB signaling pathway, purine synthesis pathway, linear ubiquitination pathway, SLC2A1, MDM2, and PIK3C3 as NPC dependency factors/pathways. Importantly, H3K27ac HiChIP linked most of these dependency factors to super-enhancers. This study provided new insight to NPC pathogenesis and also identified novel potential targets for therapy.

ORGANISM(S): synthetic construct Homo sapiens

PROVIDER: GSE123645 | GEO | 2022/11/21

REPOSITORIES: GEO

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ChIP-seq of MYST acetyltransferases

Project description:Histone acetyltransferases (HAT) assemble into multisubunit complexes in order to target distinct lysine residues on nucleosomal histones. Here, we characterize native HAT complexes assembled by the BRPF-family of scaffold proteins. Their PHD-ZnKnuckle-PHD domain is essential for binding chromatin and restricted to unmethylated H3K4, a specificity that is reversed by the associated ING subunit. Native BRPF1 complexes can contain either MOZ/MORF or HBO1 as catalytic acetyltransferase subunit. Interestingly, while the previously reported HBO1 complexes containing JADE scaffold proteins target histone H4, the HBO1-BRPF1 complex acetylates only H3 in chromatin. We mapped a small region at the N-terminus of scaffold proteins responsible for histone tail selection on chromatin. Thus, alternate choice of subunits associated with HBO1 can switch its specificity from H4 to H3 tails, highlighting a crucial new role of associated subunits within HAT complexes, previously thought to be intrinsic to the catalytic subunit.

2013-10-09 | GSE47190 | GEO

ChIP-seq of MYST acetyltransferases

2013-10-09 | E-GEOD-47190 | biostudies-arrayexpress

MYST family histone acetyltransferases in the protozoan parasite Toxoplasma gondii.

Project description:The restructuring of chromatin precedes tightly regulated events such as DNA transcription, replication, and repair. One type of chromatin remodeling involves the covalent modification of nucleosomes by histone acetyltransferase (HAT) complexes. The observation that apicidin exerts antiprotozoal activity by targeting a histone deacetyltransferase has prompted our search for more components of the histone modifying machinery in parasitic protozoa. We have previously identified GNAT family HATs in the opportunistic pathogen Toxoplasma gondii and now describe the first MYST (named for members MOZ, Ybf2/Sas3, Sas2, and Tip60) family HATs in apicomplexa (TgMYST-A and -B). The TgMYST-A genomic locus is singular and generates a approximately 3.5-kb transcript that can encode two proteins of 411 or 471 amino acids. TgMYST-B mRNA is approximately 7.0 kb and encodes a second MYST homologue. In addition to the canonical MYST HAT catalytic domain, both TgMYST-A and -B possess an atypical C2HC zinc finger and a chromodomain. Recombinant TgMYST-A exhibits a predilection to acetylate histone H4 in vitro at lysines 5, 8, 12, and 16. Antibody generated to TgMYST-A reveals that both the long and short (predominant) versions are present in the nucleus and are also plentiful in the cytoplasm. Moreover, both TgMYST-A forms are far more abundant in rapidly replicating parasites (tachyzoites) than encysted parasites (bradyzoites). A bioinformatics survey of the Toxoplasma genome reveals numerous homologues known to operate in native MYST complexes. The characterization of TgMYST HATs represents another important step toward understanding the regulation of gene expression in pathogenic protozoa and provides evolutionary insight into how these processes operate in eukaryotic cells in general.

| S-EPMC1317489 | biostudies-literature

The MYST histone acetyltransferases are essential for gametophyte development in Arabidopsis.

Project description:BackgroundHistone acetyltransferases (HATs) play critical roles in the regulation of chromatin structure and gene expression. Arabidopsis genome contains 12 HAT genes, but the biological functions of many of them are still unknown. In this work, we studied the evolutionary relationship and cellular functions of the two Arabidopsis HAT genes homologous to the MYST family members.ResultsAn extensive phylogenetic analysis of 105 MYST proteins revealed that they can be divided into 5 classes, each of which contains a specific combination of protein modules. The two Arabidopsis MYST proteins, HAM1 and HAM2, belong to a "green clade", clearly separated from other families of HATs. Using a reverse genetic approach, we show that HAM1 and HAM2 are a functionally redundant pair of genes, as single Arabidopsis ham1 and ham2 mutants displayed a wild-type phenotype, while no double mutant seedling could be recovered. Genetic analysis and cytological study revealed that ham1ham2 double mutation induced severe defects in the formation of male and female gametophyte, resulting in an arrest of mitotic cell cycle at early stages of gametogenesis. RT-PCR experiments and the analysis of transgenic plants expressing the GUS reporter gene under the HAM1 or the HAM2 promoter showed that both genes displayed an overlapping expression pattern, mainly in growing organs such as shoots and flower buds.ConclusionThe work presented here reveals novel properties for MYST HATs in Arabidopsis. In addition to providing an evolutionary relationship of this large protein family, we show the evidence of a link between MYST and gamete formation as previously suggested in mammalian cells. A possible function of the Arabidopsis MYST protein-mediated histone acetylation during cell division is suggested.

| S-EPMC2606689 | biostudies-literature

ChIP-seq of MYST acetyltransferases in RKO cell line

Project description:Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells.

2016-02-05 | GSE63722 | GEO

ChIP-seq of MYST acetyltransferases in RKO cell line

Project description:Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells. Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells.

2016-02-05 | E-GEOD-63722 | biostudies-arrayexpress

Inhibition of the MYST histone acetyltransferases KAT6A/B arrests lymphoma progression

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-08-03 | GSE108244 | GEO

Expression profiles and functional prediction of histone acetyltransferases of the MYST family in kidney renal clear cell carcinoma.

Project description:BackgroundHistone acetyltransferases (HATs) of the MYST family are associated with a variety of human cancers. However, the relationship between MYST HATs and their clinical significance in kidney renal clear cell carcinoma (KIRC) has not yet been evaluated.MethodsThe bioinformatics method was used to investigate the expression patterns and prognostic value of MYST HATs. Western blot was used to detect the expression of MYST HATs in KIRC.ResultsThe expression levels of MYST HATs except KAT8 (KAT5, KAT6A, KAT6B, and KAT7) were significantly reduced in KIRC tissues compared to normal renal tissues, and the western blot results of the KIRC samples also confirmed the result. Reduced expression levels of MYST HATs except KAT8 were significantly associated with high tumor grade and advanced TNM stage in KIRC, and showed a significant association with an unfavorable prognosis in patients with KIRC. We also found that the expression levels of MYST HATs were closely related to each other. Subsequently, gene set enrichment analysis showed that the function of KAT5 was different from that of KAT6A, KAT6B and KAT7. The expression levels of KAT6A, KAT6B and KAT7 had significant positive correlations with cancer immune infiltrates such as B cells, CD4+ T cells and CD8+ T cells.ConclusionsOur results indicated that MYST HATs, except KAT8, play a beneficial role in KIRC.

| S-EPMC10291769 | biostudies-literature

Project description:H3K27ac HiChIP libraries in PDAC

| PRJNA1070046 | ENA

H3K27ac HiChIP analysis in BALL cells

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