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

Yochum GS, McWeeney S, Rajaraman V, Cleland R, Peters S, Goodman RH
Source: Proc Natl Acad Sci USA
Publication Date: (2007)
Issue: 104(9): 3324-9
Research Area:
Cancer Research/Cell Biology
Cells used in publication:
HCT 116
Species: human
Tissue Origin: colon
Nucleofector® I/II/2b
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.