Serial analysis of chromatin occupancy identifies beta-catenin target genes in colorectal carcinoma cells

Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3324-9. doi: 10.1073/pnas.0611576104. Epub 2007 Feb 21.

Abstract

Most instances of colorectal cancer are due to abnormalities in the Wnt signaling pathway, resulting in nuclear accumulation of beta-catenin. beta-Catenin activates transcription of target genes primarily by associating with the T cell factor/lymphoid enhancer-binding factor (TCF/Lef) family of transcription factors. In this report, we use serial analysis of chromatin occupancy (SACO) to identify 412 high-confidence beta-catenin targets in HCT116 colorectal carcinoma cells. Of these targets, 84% contained a consensus TCF motif and were occupied by TCF4 in vivo. Examination of the flanking 5-bp residues in each consensus revealed motif-specific enrichment at neighboring sites. beta-Catenin binding was localized to the 5' promoters, internal regions, and 3' UTRs of protein-coding genes. Furthermore, 15 components of the canonical Wnt pathway were identified as beta-catenin target genes, suggesting that feed-forward and feedback mechanisms exist to modulate the Wnt signal in colon cancer cells.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites / genetics
  • Blotting, Western
  • Cell Line, Tumor
  • Chromatin / metabolism*
  • Chromatin Immunoprecipitation
  • Colorectal Neoplasms / genetics*
  • Computational Biology
  • Gene Expression Regulation, Neoplastic / genetics*
  • Genes / genetics*
  • Humans
  • Sequence Analysis, DNA
  • Signal Transduction / genetics*
  • TCF Transcription Factors / genetics
  • TCF Transcription Factors / metabolism*
  • Wnt Proteins / metabolism
  • beta Catenin / genetics
  • beta Catenin / metabolism*

Substances

  • Chromatin
  • TCF Transcription Factors
  • Wnt Proteins
  • beta Catenin