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Series GSE81945 Query DataSets for GSE81945
Status Public on Dec 13, 2016
Title Functional mutations form at CTCF-cohesin binding sites in melanoma due to uneven nucleotide excision repair across the motif
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary CTCF binding sites are frequently mutated in cancer, but how these mutations accumulate and whether they broadly perturb CTCF binding is not well understood. We report that skin cancers exhibit a highly-specific asymmetric mutation pattern within CTCF motifs attributable to ultraviolet irradiation and differential nucleotide excision repair (NER). CTCF binding site mutations form independent of replication timing and are enriched at sites of CTCF/cohesin complex binding, suggesting a role for cohesin in stabilizing CTCF-DNA binding and impairing NER. Performing CTCF ChIP-seq in a melanoma cell-line, we show CTCF binding site mutations to be functional by demonstrating allele-specific reduction of CTCF binding to mutant alleles. While topologically-associating domains with mutated CTCF anchors in melanoma contain differentially-expressed cancer-associated genes, CTCF motif mutations appear generally under neutral selection. However, the frequency and potential functional impact of such mutations in melanoma highlights the need to consider their impact on cellular phenotype in individual genomes.
Overall design Chromatin immunoprecipiation sequencing (ChIP-seq) against CTCF in malignant melanoma cell-line COLO829, together with IgG background control. 2 replicate experiments performed. Replicates for CTCF ChIP sequenced separately. IgG ChIP from second replicate experiment sequenced.
Contributor(s) Wong JW, Poulos RC, Thoms JA, Pimanda JE
Citation(s) 27974201
Submission date May 26, 2016
Last update date May 15, 2019
Contact name Rebecca C Poulos
Organization name UNSW Australia
Street address Level 2 ACP UNSW Australia
City Sydney
State/province NSW
ZIP/Postal code 2052
Country Australia
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (3)
GSM2178295 CTCF_1_ChIP_COLO829
GSM2178296 CTCF_2_ChIP_COLO829
GSM2178297 IgG_ChIP_COLO829
BioProject PRJNA323481
SRA SRP075768

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Supplementary file Size Download File type/resource
GSE81945_RAW.tar 800.0 Kb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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