Identification of {beta}-catenin binding regions in colon cancer cells using ChIP-Seq.
Deregulation of the Wnt/β-catenin signaling pathway is a hallmark of colon cancer. Mutations in the adenomatous polyposis coli (APC) gene occur in the vast majority of colorectal cancers and are an initiating event in cellular transformation. Cells harboring mutant APC contain elevated levels of the β-catenin transcription coactivator in the nucleus which leads to abnormal expression of genes controlled by β-catenin/T-cell factor 4 (TCF4) complexes. Here, we use chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) to identify β-catenin binding regions in HCT116 human colon cancer cells. We localized 2168 β-catenin enriched regions using a concordance approach for integrating the output from multiple peak alignment algorithms. Motif discovery algorithms found a core TCF4 motif (T/A-T/A-C-A-A-A-G), an extended TCF4 motif (A/T/G-C/G-T/A-T/A-C-A-A-A-G) and an AP-1 motif (T-G-A-C/T-T-C-A) to be significantly represented in β-catenin enriched regions. Furthermore, 417 regions contained both TCF4 and AP-1 motifs. Genes associated with TCF4 and AP-1 motifs bound β-catenin, TCF4 and c-Jun in vivo and were activated by Wnt signaling and serum growth factors. Our work provides evidence that Wnt/β-catenin and mitogen signaling pathways intersect directly to regulate a defined set of target genes.
Bottomly
Daniel
D
Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR, USA.
Kyler
Sydney L
SL
McWeeney
Shannon K
SK
Yochum
Gregory S
GS
D001665:Binding Sites; D002352:Carrier Proteins / Q000235:genetics; D045744:Cell Line, Tumor; D002843:Chromatin / Q000737:chemistry; D047369:Chromatin Immunoprecipitation; D003110:Colonic Neoplasms / Q000235:genetics*; D004268:DNA-Binding Proteins; D023281:Genomics; D006801:Humans; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D014157:Transcription Factors; D051176:beta Catenin / Q000378:metabolism*
C540448:CXXC5 protein, human; D002352:Carrier Proteins; D002843:Chromatin; D004268:DNA-Binding Proteins; D014157:Transcription Factors; D051176:beta Catenin
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