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Series GSE47590 Query DataSets for GSE47590
Status Public on Feb 03, 2015
Title 5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [seq]
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The discovery of cytosine hydroxymethylation (5-hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behavior in colon cancer. 5-hmC is globally reduced in proliferating cells such as colon tumors and the gut crypt progenitors, from which tumors can arise. Here, we show that colorectal tumors and cancer cells express Ten-Eleven Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5-hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5-hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells. Together our results indicate that promoters that acquire 5-hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5-hmC in tumors. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation.
 
Overall design 5 normal colon samples and 4 matching tumor samples were profiled for 5-hydroxymethylcytosine content genomewide using hmeDIP-seq.
The colorectal cancer cell line HCT116 was profiled for binding of TET2 genomewide by chromatin immunoprecipitation sequencing (ChIP-seq).
 
Contributor(s) Uribe-Lewis S, Stark R, Carroll T, Dunning M, Halim S, Vowler S
Citation(s) 25853800
Submission date Jun 03, 2013
Last update date May 15, 2019
Contact name Chandra Chilamakuri
E-mail(s) datasubmissions@cruk.cam.ac.uk
Organization name Cancer Research UK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL15456 Illumina HiScanSQ (Homo sapiens)
Samples (17)
GSM1152863 24_NA_bound
GSM1152864 42_NC_bound
GSM1152865 24_NC_bound
This SubSeries is part of SuperSeries:
GSE47592 5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer
Relations
BioProject PRJNA206436
SRA SRP023528

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE47590_RAW.tar 15.3 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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