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Series GSE41820 Query DataSets for GSE41820
Status Public on Oct 24, 2012
Title High-resolution genome-wide mapping of AHR and ARNT binding sites by ChIP-Seq
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The aryl hydrocarbon receptor (AHR) and AHR nuclear translocator (ARNT) activated complex regulates genes in response to the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). AHR has also emerged as a potential therapeutic target for the treatment of human diseases and different cancers, including breast cancer. To better understand AHR and ARNT signaling in breast cancer cells, we used chromatin immunoprecipitation linked to high throughput sequencing to identify AHR- and ARNT-binding sites across the genome in TCDD treated MCF-7 cells. We identified 2,594 AHR-bound, 1,352 ARNT-bound and 882 high confidence AHR/ARNT co-bound regions. No significant differences in the genomic distribution of AHR and ARNT were observed. Approximately 60% of the co-bound regions contained at least one core AHRE, 5'-GCGTG-3'. AHR/ARNT peak density was the highest within 1 kb of transcription start sites (TSS); however, a number of AHR/ARNT co-bound regions were located as far as 100 kb from TSS. De novo motif discovery identified a symmetrical variation of the AHRE (5'-GTGCGTG-3'), as well as FOXA1 and SP1 binding motifs. Microarray analysis identified 104 TCDD responsive genes where 98 genes were up-regulated by TCDD. Of the 104 regulated genes, 69 (66.3%) were associated with an AHR- or ARNT-bound region within 100 kb of their TSS. Overall our study identified AHR/ARNT co-bound regions across the genome, revealed the importance but not absolute requirement for an AHRE in AHR/ARNT interactions with DNA, and identified a modified AHRE motif, thereby increasing our understanding of AHR/ARNT signaling pathway.
 
Overall design Examination of genome-wide AHR and ARNT binding pattern in MCF-7
 
Contributor(s) Lo R, Matthews J
Citation(s) 22903824
Submission date Oct 24, 2012
Last update date May 15, 2019
Contact name Raymond Lo
E-mail(s) r.lo@mail.utoronto.ca
Organization name University of Toronto
Department Pharmacology
Lab Matthews
Street address 1 King's College Circle Rm 4336
City Toronto
State/province Ontario
ZIP/Postal code M5G2M4
Country Canada
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (4)
GSM1024799 AHR_ChIP-Seq
GSM1024800 ARNT_ChIP-Seq
GSM1024801 IgG_negative_control [reps 1 and 3]
Relations
BioProject PRJNA178231
SRA SRP016797

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
GSE41820_RAW.tar 50.0 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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