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Alterations in chromosome spatial compartmentalization classify prostate cancer progression [array]

ABSTRACT: Alterations in chromosome spatial compartmentalization classify prostate cancer progression [array]

PROVIDER: PRJNA722012 | ENA |

REPOSITORIES: ENA

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Alterations in chromosome spatial compartmentalization classify prostate cancer progression.

Project description:Alterations in chromosome spatial compartmentalization classify prostate cancer progression.

| PRJNA722007 | ENA

Alterations in chromosome spatial compartmentalization classify prostate cancer progression [Hi-C]

Project description:Alterations in chromosome spatial compartmentalization classify prostate cancer progression [Hi-C]

| PRJNA722011 | ENA

Alterations in chromosome spatial compartmentalization classify prostate cancer progression [array]

Project description:Through a systematic analysis of chromosome conformation capture in a cohort of cells that model cancer progression, San Martin et.al. find that rearrangement of the 3D genome structure in prostate cancer is a potential mechanism for disease exacerbation and that genome-wide compartment identity can classify cancer according to progression

2021-05-01 | GSE172098 | GEO

Alterations in chromosome spatial compartmentalization classify prostate cancer progression [Hi-C]

2021-05-01 | GSE172097 | GEO

Alterations in chromosome spatial compartmentalization classify prostate cancer progression.

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

2021-05-01 | GSE172099 | GEO

Spatial Compartmentalization at the Nuclear Periphery Characterized by Genome-wide Mapping

Project description:How gene positioning to the nuclear periphery regulates transcription remains largely unclear. We have previously observed the differential compartmentalization of transcription factors and histone modifications at the nuclear periphery in mouse C2C12 myoblasts. Here, we have integrated high throughput DNA sequencing into the DNA adenine methyltransferase identification (DamID) assay, and have identified ~15, 000 sequencing-based Lamina-Associated Domains (sLADs) in mouse 3T3 fibroblasts and C2C12 myoblasts. These genomic regions range from a few kb to over 1 Mb and cover ~30% of the genome, and are spatially proximal to the nuclear lamina (NL). Active histone modifications such as H3K4me2, H3K9Ac, H3K36me3 and H3K79me2 are all localized away from the nuclear periphery microscopically, and distributed predominantly out of sLADs genome-wide. Therefore, the spatial compartmentalization of active histone modifications likely characterizes a major portion of chromatin at the nuclear periphery in mammalian cells. Genomic regions around transcription start sites of expressed sLAD genes display reduced associations with the NL and possess active histone modifications; in contrast, gene bodies of expressed sLAD genes possess very low levels of active histone modifications. Our genome-wide analyses of NL-associated chromatin have enabled functional and mechanistic dissections of gene positioning on transcription regulation. generate DamID maps of genome-NL interaction for mouse 3T3 fibroblasts and C2C12 myoblasts

2013-10-30 | E-GEOD-41583 | biostudies-arrayexpress

Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression.

Project description:Prostate cancer aggressiveness and metastatic potential are influenced by gene expression and genomic aberrations, features that can be influenced by the 3D structure of chromosomes inside the nucleus. Using chromosome conformation capture (Hi-C), we conducted a systematic genome architecture comparison on a cohort of cell lines that model prostate cancer progression, from normal epithelium to bone metastasis. We describe spatial compartment identity (A-open versus B-closed) changes with progression in these cell lines and their relation to gene expression changes in both cell lines and patient samples. In particular, 48 gene clusters switch from the B to the A compartment, including androgen receptor, WNT5A, and CDK14. These switches are accompanied by changes in the structure, size, and boundaries of topologically associating domains (TADs). Further, compartment changes in chromosome 21 are exacerbated with progression and may explain, in part, the genesis of the TMPRSS2-ERG translocation. These results suggest that discrete 3D genome structure changes play a deleterious role in prostate cancer progression. .

| S-EPMC8669499 | biostudies-literature

Spatial Compartmentalization at the Nuclear Periphery Characterized by Genome-wide Mapping

2013-10-30 | GSE41583 | GEO

Spatial transcriptomics reveals functional compartmentalization of mucinous colorectal adenocarcinoma

Project description:We performed spatial transcriptomics to profile compositional and spatial distribution of hetergeneous cell populations in mucinous colorectal adenocarinoma

2024-04-28 | GSE236697 | GEO

A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina

Project description:This SuperSeries is composed of the following subset Series: GSE35777: A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [Tiling Array] GSE36048: A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [ChIP-seq] Refer to individual Series

2012-02-24 | E-GEOD-36049 | biostudies-arrayexpress

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