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The ZMYND8-regulated Mevalonate Pathway Endows YAP-High Intestinal Cancer with Metabolic Vulnerability

ABSTRACT: To elucidate the molecular basis by which ZMYND8 influences intestinal stemness and tumorigenesis, we performed RNA-seq to analyze gene expression in the crypts of 2-month-old Apcmin/+ and Apcmin/+; Zmynd8IEC–/– mice. Next, we performed chromatin immunoprecipitation (ChIP) sequencing (ChIP-Seq) to characterize the genomic distribution of ZMYND8 and SREBP2 in HCT116 WT and SREBP2-KO cells under sterol-depleted conditions.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE151804 | GEO | 2021/04/21

REPOSITORIES: GEO

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The ZMYND8-regulated Mevalonate Pathway Endows YAP-High Intestinal Cancer with Metabolic Vulnerability

Project description:The ZMYND8-regulated Mevalonate Pathway Endows YAP-High Intestinal Cancer with Metabolic Vulnerability

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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

Transcriptome profiling of control and Zmynd8-cKO mouse cardiomyocyte

Project description:Appropriate gene expression within cardiomyocytes is coordinated by chromatin factors and is essential for heart function. We investigated the role of the chromatin reader ZMYND8 in the mouse heart using null and conditional knockouts (Zmynd8-cKO). While full-length Zmynd8 is not required for cardiomyocyte development, Zmynd8-cKO mice develop cardiomegaly, decreased cardiac function, and premature death compared to controls. Transcriptome analysis of Zmynd8-cKO cardiomyocytes reveals illegitimate expression of transcripts and proteins normally limited to skeletal muscle and integration of TNNI2 skeletal troponin into cardiac sarcomeres of mutant mice. We conclude that ZMYND8 is necessary to maintain appropriate cardiomyocyte homeostasis and gene expression.

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Microarray upon ZMYND8 knockdown in Hela cells

Project description:ZMYND8, a chromatin reader/effector protein, knockdown in Hela cells

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Microarray upon ZMYND8 knockdown in MCF7 cells

Project description:ZMYND8, a chromatin reader/effector protein, knockdown in MCF7 cells

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Gene expression change after targeted degradation of ZMYND8 or IRF8

Project description:Cancer cell type-selective addiction of transcription-chromatin regulatory program provides opportunities for therapeutic interventions. Here, we uncovered an IRF8-MEF2D transcription factor (TF) regulatory circuit as an acute myeloid leukemia (AML)-biased dependency. Combining CRISPR-based genetic screens, transcriptional analysis, and chromatin profiling, we demonstrated that a chromatin regulator, ZMYND8, directly regulates IRF8 and MYC expression through occupying AML-specific enhancer regions. ZMYND8 was essential for AML proliferation both in vitro and in vivo. The ZMYND8-occupied IRF8 enhancer was further characterized using Circular Chromosome Conformation Capture and CRISPRi-based perturbation assays and was observed in primary patient cells. Importantly, mutagenesis experiments revealed that the PHD/Bromodomain/PWWP reader module is required for ZMYND8 tethering to leukemia-essential co-activator BRD4 for enhancer-mediated gene regulation. Our results rationalize ZMYND8 as a potential selective therapeutic target for modulating the IRF8/MYC transcriptional networks in AML.

2021-09-06 | GSE157633 | GEO

Gene expression change after inactivation of ZMYND8 by CRISPR-Cas9

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Regulation of 27-hydroxycholesterol metabolism by ZMYND8

Project description:ZMYND8 is a master regulator of 27-hydroxycholesterol metabolism in breast cancer stem cells.

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¬¬ZMYND8 co-localizes with NuRD on target genes and regulates poly-ADP-ribose dependent recruitment of GATAD2A/NuRD to sites of DNA damage

Project description:The NuRD complex is generally thought to repress transcription at both hyper- and hypomethylated regions in the genome. In addition, the complex is involved in the DNA damage response. Here, we show that ZMYND8 bridges NuRD to a number of putative DNA-binding zinc finger proteins. The ZMYND8 MYND domain directly interacts with PPPLΦ motifs in the NuRD subunit GATAD2A. Furthermore, GATAD2A and GATAD2B exclusively form homodimers and they thus define mutually exclusive NuRD subcomplexes. ZMYND8 and MBD3 share a large number of genome-wide binding sites, mostly active promoters and enhancers. Depletion of ZMYND8 does not affect NuRD occupancy genome-wide and expression of NuRD/ZMYND8 target genes in steady-state asynchronous cells. However, ZMYND8 facilitates immediate recruitment of GATAD2A/NuRD to induced sites of DNA damage in a PAR-dependent manner. These results thus show that a specific substoichiometric interaction with a NuRD subunit paralogue provides unique functionality to a distinct NuRD subcomplex.

2016-10-10 | PXD003856 | Pride

Regulation of hypoxia-inducible factor activity by ZMYND8

Project description:ZMYND8 coactivates the global HIF target genes in breast cancer MDA-MB-231 cells.

2019-04-10 | GSE108833 | GEO