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The effects of the global loss of DNA methylation on the functional cancer epigenome (Bisulfite-seq)

ABSTRACT: We compare the global DNA methylation and nucleosome occupancy patterns of HCT116 colon cancer cells with its genetic derivatives DKO1 cells which lack DNMT3B and DNMT1 activity

ORGANISM(S): Homo sapiens

PROVIDER: GSE58695 | GEO | 2015/02/06

SECONDARY ACCESSION(S): PRJNA253190

REPOSITORIES: GEO

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The effects of the global loss of DNA methylation on the functional cancer epigenome (Bisulfite-seq)

Project description:We compare the global DNA methylation and nucleosome occupancy patterns of HCT116 colon cancer cells with its genetic derivatives DKO1 cells which lack DNMT3B and DNMT1 activity Simultaneous genome-wide mapping of DNA methylation and nucleosome occupancy of HCT116 and DKO1 cells using NOMe-seq, rep2

2015-02-06 | E-GEOD-58695 | biostudies-arrayexpress

The effects of the global loss of DNA methylation on the functional cancer epigenome

Project description:We compare the global histone modification patterns of HCT116 colon cancer cells with its genetic derivatives DKO1 cells which lack DNMT3B and DNMT1 activity

2015-02-06 | GSE58638 | GEO

The effects of the global loss of DNA methylation on the functional cancer epigenome

Project description:We compare the global histone modification patterns of HCT116 colon cancer cells with its genetic derivatives DKO1 cells which lack DNMT3B and DNMT1 activity Comparison of histone marks in two cell types

2015-02-06 | E-GEOD-58638 | biostudies-arrayexpress

DNA methylation screening identifies driver epigenetic events of cancer cell survival.

Project description:Genome wide DNA methylation profiling of colon adenocarcinoma cell line HCT116 wild type and with a genetic disruption of DNMT3B and DNMT1 (DKO). The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. For this study, we used two DKO subclones, DKO8 and DKO1, which retain approximately 45% and 5% of the HCT116 wild type global DNA methylation levels, respectively

2012-03-16 | GSE36534 | GEO

DNA methylation screening identifies driver epigenetic events of cancer cell survival.

2012-03-16 | E-GEOD-36534 | biostudies-arrayexpress

Comparative analyses of the N-glycoproteomes in HCT116 cancer cells and their non-tumorigenic DNMT1/3b double knockout (DKO1) cells and insight into the Mannose-6-phosphate pathway

Project description:N-glycoproteomic analyses provide valuable resources for investigation of cancer mechanisms, biomarkers, and therapeutic targets. Here, we mapped and compared the site-specific N-glycoproteomes of colon cancer HCT116 cells and isogenic non-tumorigenic DNMT1/3b double knockout (DKO1) cells using Fbs1-GYR N-glycopeptide enrichment technology and trapped ion mobility spectrometry. Many significant changes in site-specific N-glycosylation were revealed, providing a molecular basis for further elucidation of the role of N-glycosylation in protein function. HCT116 cells display hypersialylation especially in cell surface membrane proteins. Both HCT116 and DKO1 show an abundance of paucimannose and 80% of paucimannose-rich proteins are annotated to reside in exosomes. The most striking N-glycosylation alteration was the degree of mannose-6-phosphate (M6P) modification. N-glycoproteomic analyses revealed that HCT116 display hyper-M6P modification, which was orthogonally validated by M6P immunodetection. Significant observed differences in N-glycosylation patterns of the major M6P receptor, CI-MPR in HCT116 and DKO1 may contribute to the hyper-M6P phenotype of HCT116 cells.

2023-01-17 | PXD035301 | Pride

RNA-seq of HCT116 and HCT116-DKO colon cancer cell lines

Project description:RNA-seq was performed on parental HCT116 colon cancer cell line and on HCT116 DKO (double knock-out) cell line, which contains genetic knockouts of both DNA methyltransferases DNMT1 (-/-) and DNMT3b (-/-).

2019-06-07 | GSE82338 | GEO

DNMT DKO proteomic analyses - A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

Project description:This study aimed to investigate the link between DNA methylation and protein expression on a genome wide level, using a combination of MBD-sequencing and shotgun and positional proteomics on two human colon cancer cell lines: a wild type HCT116 cell line and a double knock out HCT116 cell line (DNMT1 -/- and DNMT3b -/-). The protein content of the HCT116 WT and DKO cell lines was not only analyzed using a standard shotgun proteomics approach, but also with the N-terminal COFRADIC technique (Staes et al., 2011), in order to determine the (alternative) translation start site of the expressed proteins.

2015-08-19 | PXD000304 | Pride

Protect-seq: Genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin

Project description:We compare histone modifications, chromatin accessibility, and replication timing domain genome-wide in HCT116 colon cancer cells with its genetic derivative DKO cells which lack DNMT3B and DNMT1 activity and the fibrosarcoma cell line HT1080.

2019-11-25 | GSE135580 | GEO

Global loss of DNA methylation uncovers intronic enhancers in genes

Project description:We used HCT116 colorectal cancer cells with and without mutations in DNA methyltransferases (resulting in a 95% reduction in global DNA methylation levels) to study the relationship between DNA methylation, histone modifications, and gene expression. (The double knockout cell line is called DKO1) Examination of DNA methylation, two histone modifications, RNA polymerase II ChIP-seq and RNA expression in two cell line (HCT116 and DKO1). One of relipates of HCT116 RNA P II ChIP-seq is from GSM970210. Histone modification data(H3K27ac, H3K4me3) of HCT116 are from GSM945304, GSE31755. Two replicates of RNA-seq data in HCT116 are from GSM1266733 and GSM1266734

2014-09-10 | E-GEOD-60106 | biostudies-arrayexpress

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