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ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genes

ABSTRACT: Histone acetylation, including acetylated H3K14 (H3K14ac), is generally linked to gene activation. Monomethylated histone H3 lysine 4 (H3K4me1), together with other gene-activating marks, denotes active genes. In contrast to usual gene-activating functions of H3K14ac and H3K4me1, we here show that the dual histone modification mark H3K4me1-H3K14ac is recognized by ZMYND8 (also called RACK7) and functions to counteract gene expression. We identified ZMYND8 as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 antagonizes the expression of metastasis-linked genes, and its knockdown increases the cellular invasiveness in vitro and in vivo. The plant homeodomain (PHD) and Bromodomain cassette in ZMYND8 mediates the combinatorial recognition of H3K4me1-H3K14ac and H3K4me0-H3K14ac by ZMYND8. These findings uncover an unexpected role for the signature H3K4me1-H3K14ac in attenuating gene expression and reveal a previously unknown metastasis-suppressive epigenetic mechanism in which ZMYND8's PHD-Bromo cassette couples H3K4me1-H3K14ac with repression of metastasis-linked genes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE82260 | GEO | 2016/07/28

SECONDARY ACCESSION(S): PRJNA324450

REPOSITORIES: GEO

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ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genes

Project description:Histone acetylation, including acetylated H3K14 (H3K14ac), is generally linked to gene activation. Monomethylated histone H3 lysine 4 (H3K4me1), together with other gene-activating marks, denotes active genes. In contrast to usual gene-activating functions of H3K14ac and H3K4me1, we here show that the dual histone modification mark H3K4me1-H3K14ac is recognized by ZMYND8 (also called RACK7) and functions to counteract gene expression. We identified ZMYND8 as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 antagonizes the expression of metastasis-linked genes, and its knockdown increases the cellular invasiveness in vitro and in vivo. The plant homeodomain (PHD) and Bromodomain cassette in ZMYND8 mediates the combinatorial recognition of H3K4me1-H3K14ac and H3K4me0-H3K14ac by ZMYND8. These findings uncover an unexpected role for the signature H3K4me1-H3K14ac in attenuating gene expression and reveal a previously unknown metastasis-suppressive epigenetic mechanism in which ZMYND8's PHD-Bromo cassette couples H3K4me1-H3K14ac with repression of metastasis-linked genes. i) ChIP-Seq data of ZMYND8, JARID1D, H3K4me1, H3K14ac, H3K4me3, and H3K27me3 in normal DU145 cells. ii) ChIP-Seq data of H3K4me1 and H3K4me3 in shLuciferase-, shJARID1D-, or shZMYND8-treated DU145 cells. iii) RNA-Seq data in shLuciferase-, shJARID1D-, or shZMYND8-treated DU145 cells.

2016-07-28 | E-GEOD-82260 | biostudies-arrayexpress

Homo sapiens

Project description:ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genes

| PRJNA324450 | ENA

Homo sapiens

Project description:Multivalent histone and DNA engagement by a PHD/BRD/PWWP triple reader cassette recruits ZMYND8 to K14ac-rich chromatin

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Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis [RNA-Seq]

Project description:Chromatin remodeling and histone modifications are important for development and floral phase transition in plants. However, it is largely unknown whether and how these two epigenetic regulators coordinately regulate the important biological processes. Here, we identified three types of ISWI chromatin remodeling complexes in Arabidopsis thaliana. We found that ARID5, a subunit of a plant-specific ISWI complex, can regulate development and floral phase transition. The ARID-PHD dual domain cassette of ARID5 recognizes both the H3K4me3 histone mark and AT-rich DNA. We determined the ternary complex structure of the ARID5 ARID-PHD cassette with an H3K4me3 peptide and an AT-containing DNA. The H3K4me3 peptide is combinatorially recognized by the PHD and ARID domains, while the DNA is specifically recognized by the ARID domain. Both PHD and ARID domains are necessary for the association of ARID5 with chromatin. The results suggest that the dual recognition of AT-rich DNA and H3K4me3 by the ARID5 ARID-PHD cassette may facilitate the association of the ISWI complex with specific chromatin regions to regulate development and floral phase transition

2019-11-01 | GSE139637 | GEO

Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis [ChIP-Seq]

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Multivalent histone and DNA engagement by the triple reader module of ZMYND8 directs the recruitment of a transcriptional network to genes to regulate gene expression

Project description:Elucidation of multivalent interactions involving both DNA and histone post-translational-modifications (PTMs) is essential for providing insight into complex biological functions. We report here the high resolution crystal structure of the N-terminal triple reader module (PHD-Bromo-PWWP) of ZMYND8, which forms a stable unit, capable of simultaneously recognizing histone PTMs and providing a charged platform for DNA interaction. Monte Carlo simulations provide a model whereby the reader module directly engages the core nucleosome particle, extracting the entire histone H3 tail and initiating contacts with the DNA super-coil structure. Systematic mutation of these interaction interfaces reveals cooperativity within the ensemble. Single domain disruption destroys the functional network of interactions initiated by ZMYND8, which impairs recruitment to sites of DNA damage and alters transcription. Taken together, our results establish an important role of the ZMYND8 multivalent reader module in nucleosome binding and chromatin function.

2021-04-30 | GSE75624 | GEO

The complex pattern of epigenomic variation between natural yeast strains at single-nucleosome resolution

Project description:We investigated natural inter-individual variation of the epigenome in a quantitative manner. To probe the degree of natural epigenomic diversity in S. cerevisiae, we compared three unrelated wild strains using replicated Mnase-seq and ChIP-seq profiling at mononucleosomal resolution for five histone marks (H3K4me3, H3K9ac, H3K14ac and H4K12ac and H3K4me1).

2015-07-21 | E-MTAB-3390 | biostudies-arrayexpress

RNA-sequencing of GmPHD6 over-expression and RNAi transgenic hairy roots and the control samples of K599

Project description:Plant homeodomain (PHD) finger proteins are ‘histone code readers’. They recognize and bind to epigenetically modified histone H3 ‘tail’. Here we reported that an Alfin1-like soybean protein, GmPHD6, read H3K4me0/1/2 but not H3K4me3 with the N-terminal instead of the PHD finger. GmPHD6 does not possess transcriptional regulatory ability. Through the PHD finger, GmPHD6 interacts with its co-activator, LHP1-1/2. Using a transgenic hairy root system, we demonstrated that over-expression of GmPHD6 improved stress tolerance in transgenic soybean composites. Perhaps due to the excessive amount of LHP1 compared to that of GmPHD6, over-expression of LHP1-1/2 failed to do so. The integrity of the complex is essential in stress response, for the abrogation of DNA binding activity of GmPHD6 or the decrease of LHP1 content leads to stress sensitivity in soybean. GmPHD6 influences expression of dozens of stress-related genes to confer stress tolerance. Among these genes, we identified three direct targets of GmPHD6, ASR (ABA-stress-ripening induced), CYP71A22 (cytochrome P450) and CYP82C4. Our study reveals significant findings in stress response. GmPHD6 and LHP1 are recruited to H3K4me0/1/2 marks, where several stress-related genes may locate in, to form a transcriptional activation complex. GmPHD6 locates target sites through recognizing the G-rich elements in their promoters; LHP1 enhances expression levels of these targets. Genetically engineering of GmPHD6/LHP1 complex should improve stress tolerance in crop plants.

2018-02-13 | GSE85077 | GEO

yeats cells AP-MS for Jhd2 and Tpk2 relative to article Phosphorylation of Jhd2 by the Ras-cAMP- PKA pathway regulates histone modifications and autophagy

Project description:This work uncovers a novel and biologically significant mechanism that directly connects nutrient availability to histone modifications and gene transcription. We report that glycolysis promotes histone H3K4 trimethylation (H3K4me3) by activating Tpk2, a catalytic subunit of protein kinase A (PKA) via the Ras-cyclic AMP (cAMP) pathway. Glucose-activated PKA (Tpk2) inhibits Jhd2-catalyzed H3K4 demethylation by phosphorylating Jhd2 at serine 321 and serine 340. In addition, Tpk2- catalyzed Jhd2 phosphorylation promotes H3K14ac by preventing the binding of Rpd3 at chromatin.

2022-08-29 | PXD030815 | Pride

Multivalent histone and DNA engagement by a PHD/BRD/PWWP triple reader cassette recruits ZMYND8 to K14ac-rich chromatin

Project description:Elucidation of interactions involving DNA and histone post-translational-modifications (PTMs) is essential for providing insight into complex biological functions. Reader assemblies connected via flexible linkages facilitate avidity and increase affinity, however little is known of the contribution to the recognition process of multiple PTMs due to rigidity in the absence of conformational flexibility. We report here the high resolution crystal structure of the triple-reader module (PHD-Bromo-PWWP) of ZMYND8 which forms a stable unit capable of simultaneously recognizing multiple histone PTMs, while presenting a charged platform for association with DNA. Single domain disruptions destroy the functional network of interactions initiated by ZMYND8, impairing recruitment to sites of DNA damage. Our data establish proof-of-principle that rigidity can be compensated by concomitant DNA and histone PTM interactions, maintaining multivalent engagement of transient chromatin states, thus identifying an important underappreciated role for rigid multivalent reader modules in nucleosome binding and chromatin function.

2016-11-23 | GSE81696 | GEO

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