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Anti-cancer drugs curaxins target the 3D genome organization [HiC]

ABSTRACT: Anti-cancer drugs curaxins target the 3D genome organization [HiC]

PROVIDER: PRJNA482566 | ENA |

REPOSITORIES: ENA

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Anti-cancer drugs curaxins target the 3D genome organization [HiC]

Project description:We have recently discovered a class of anti-cancer agents, curaxins, which suppress transcription of oncogenes. Here we demonstrate that curaxins preferentially downregulate expression of genes controlled by enhancers and super-enhancers via interrupting enhancer/promoter spatial communication. Our observations made both on a model of enhancer-regulated transcription of chromatinized template and on cultured cancer cells allow classifying curaxins as a novel type of epigenetic drugs that target the 3D genome organization.

2019-02-18 | GSE117582 | GEO

Anti-cancer drugs curaxins target the 3D genome organization

Project description:Anti-cancer drugs curaxins target the 3D genome organization

| PRJNA505307 | ENA

Anti-cancer drugs curaxins target the 3D genome organization [ChIP-seq]

2019-02-18 | GSE122462 | GEO

Anti-cancer drugs curaxins target the 3D genome organization [ChIP-seq]

Project description:Anti-cancer drugs curaxins target the 3D genome organization [ChIP-seq]

| PRJNA505308 | ENA

Nuclear speckles as a key regulator for the 3D genome organization [HiC]

Project description:Nuclear speckles as a key regulator for the 3D genome organization [HiC]

| PRJNA543774 | ENA

Regulation of 3D genome organization, transcription and histone H3K9me2 by histone H3K9 methyltransferases [HiC]

Project description:Regulation of 3D genome organization, transcription and histone H3K9me2 by histone H3K9 methyltransferases [HiC]

| PRJNA715217 | ENA

Anti-cancer drugs curaxins target the 3D genome organization

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

2019-02-18 | GSE122463 | GEO

Regulation of 3D genome organization, transcription and histone H3K9me2 by histone H3K9 methyltransferases [HiC]

Project description:Histone H3 lysine 9 dimethylation (H3K9me2) is a highly conserved silencing epigenetic mark. Chromatin marked with H3K9me2 forms large domains in mammalian cells and overlaps well with lamina-associated domains and the B compartment defined by Hi-C. However, the role of H3K9me2 in 3-dimensional (3D) genome organization remains unclear. We investigated genome-wide H3K9me2 distribution, transcriptome, and 3D genome organization in mouse embryonic stem cells following the inhibition or depletion of five H3K9 methyltransferases (MTases): G9a, GLP, SETDB1, SUV39H1, and SUV39H2. H3K9me2 was regulated by all five MTases; however, H3K9me2 and transcription in the A and B compartments were regulated by different MTases. H3K9me2 in A compartments was primarily regulated by G9a/GLP and SETDB1, while H3K9me2 in the B compartments was regulated by all five MTases. Furthermore, decreased H3K9me2 correlated with changes to the more active compartmental state that accompanied transcriptional activation.

2021-03-18 | GSE169103 | GEO

HiC-sequencing in human monocyte differentiation (3D-MO)

Project description:This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.

2022-06-24 | E-MTAB-10848 | biostudies-arrayexpress

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [HiC]

Project description:Genome-wide rhythmic occupancy of RNA polymerase II (RNAPII) is highly coordinated with rhythmic genes expression. Rhythmic RNAPII binding dynamically modulates diurnal 3D genome architecture remodeling with 91% of the chromatin interactions were altered. The rhythmic genes cluster at the 8:00 (AM) circadian phase form spatial interacting clusters in turn assist coordinated rhythmic gene expression, while non-rhythmic genes tend to tether together and contribute to expression at 20:00 (PM) circadian window. Target genes and associated cis-binding motifs of transcription factors enrichment points to the existence of subnuclear organization hub enriched around the TFs. RNAPII-associated chromatin interaction domains (CIDs) are under circadian control, and static CIDs with common node genes but changed connecting genes along the circadian cycle, reveal they may function as distinct clock components in the interconnected circuits between morning and evening. Core circadian clock genes related chromatin connectivity networks reveal a compact and highly connected chromatin architecture serving to coordinate gene expression in the morning, whereas a scattered, loose chromatin architecture coordinates PM gene expression. Our findings uncover novel diurnal fundamental genome folding principles in plants, and reveal the distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.

2022-12-23 | GSE221374 | GEO

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