Bioinformatics Software Development Projects

Genome-wide Location Analysis of b-catenin/TCF Target Genes using Custom Human Promoter Microarray

Principal Investigator: Chunming Liu, University of Texas Medical Branch
Funding agency: UTMB start-up fund

Wnt/b-catenin signaling plays essential roles in both development and tumorigenesis (Moon et al. 2004). Wnt signaling is mediated by b-catenin, which binds T cell factor (TCF) in the nucleus and activates gene transcription. In the absence of Wnt stimulation, a protein complex consisting of Glycogen synthase kinase-3 (GSK-3), Casein kinase I alpha (CKIa) and tumor suppressor proteins Axin and Adenomatous polyposis coli (APC), phosphorylates b-catenin (Liu et al. 2002). The phosphorylated b-catenin is degraded by the ubiquitin/proteasome pathway (Liu et al. 1999). However, mutations in the Wnt/b-catenin signaling pathway prevent b-catenin degradation (Liu et al. 2002). Accumulated b -catenin enters the nucleus and forms a complex with TCF and activates TCF target genes that ultimately lead to tumor formation, e.g. colorectal cancers. Although gene expression microarray studies have revealed some b-catenin/TCF related genes, many of them are actually not regulated by b-catenin/TCF directly. To identify the complete direct target genes that b-catenin/TCF transcribes, a custom human promoter array has been designed locating all possible candidate TCF binding sites throughout the human genome. 60-mer probes are specifically designed based on GC-content, complexity, self-binding and uniqueness. Probes are submitted to Agilent Technologies and the custom array is manufactured by SurePrint technology. ChIP-on-chip analysis is being performed in human colon cancer cell lines using antibody against TCF4 and a high resolution map of b-catenin/TCF target genes and the genetic b-catenin/TCF regulatory network are under construction and characterization.

Bioinformatics Home