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Series GSE56051 Query DataSets for GSE56051
Status Public on Sep 26, 2014
Title Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Alterations in chromatin modifications, including DNA methylation and histone modification patterns, have been characterized under exposure of several environmental pollutants, including nickel. As with other carcinogenic metals, the mutagenic potential of nickel compounds is low and is not well correlated with its carcinogenic effects. Nickel exposure, however, is associated with alterations in chromatin modifications and related transcriptional programs, suggesting an alternative pathway whereby nickel exposure can lead to disease. To investigate the extent to which nickel exposure disrupts chromatin patterns, we profiled several histone modifications, including H3K4me3, H3K9ac, H3K27me3 and H3K9me2 as well as the insulator binding protein CTCF and the transcriptomes of control BEAS-2B cells and cells treated with nickel for 72 hours. Our results show significant alterations of the repressive histone modification H3K9me2 in nickel-exposed cells with spreading of H3K9me2 into new domains associated with gene silencing. We furthermore show that local regions of active chromatin can protect genes from nickel-induced H3K9me2 spreading. Interestingly, we show that nickel exposure selectively disrupts weaker CTCF sites, leading to spreading of H3K9me2 at these regions. These results have major implications in the understanding of how environmental carcinogens can affect chromatin dynamics and the consequences of chromatin domain disruption in disease progression.
Overall design Treat BEAS-2B cells with NiCl2 for 72 hours and compare histone modification, CTCF binding to control BEAS-2B cells to see how they regulated gene expression by RNA-seq
Contributor(s) Schones DE, Cuddapah S, Xu B, Jose C
Citation(s) 25246589
Submission date Mar 20, 2014
Last update date May 15, 2019
Contact name Dustin E Schones
Phone +1-626-471-9319
Organization name City of Hope
Department Cancer Biology
Lab Schones
Street address 1500 Duarte Rd
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (12)
GSM1354430 H3K4me3_ChIPSeq_Control
GSM1354431 H3K4me3_ChIPSeq_Nickel
GSM1354432 H3K9me2_ChIPSeq_Control
This SubSeries is part of SuperSeries:
GSE56053 Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption
BioProject PRJNA242309
SRA SRP040326

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
GSE56051_RAW.tar 2.2 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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