title: Genome-wide ChIP-seq analysis of TCF4 binding regions in colorectal cancer cells.
abstract: OBJECTIVE
  TCF4 (transcriptional factor 4) forms a complex with its transcriptional coactivator β-catenin and the coactivator carries the final signal output from the canonical Wnt signaling pathway, which is essential for the growth of normal epithelium and also plays important roles in carcinogenesis of colon epithelium. We aimed to gain a better understanding of the genes bound by TCF4 in colorectal cancer cells.
  
  
  METHODS
  SW620 human colorectal cancer cells were cultured. The TCF4 antibody of this study was confirmed in SW620 cells by Western Blot. A ChIP-seq based genome-wide analysis of TCF4 chromatin occupancy in colorectal cancer cells was conducted and 1506 high confidence TCF4 binding sites wereidentified.
  
  
  RESULTS
  Sequence analysis revealed that the binding sites harbor a consensus sequence of C-G/C-A-G-C-T/C-C-T-T-C. Gene ontology and pathway analysis showed that TCF4 regulated 18 genes in Wnt signaling pathway and 97 other transcription factors.
  
  
  CONCLUSIONS
  Our results suggest TCF4 binding regions were enriched with a motif of C-G/C-A-G-C-T/C-C-T-T-C. The gene regulation of TCF4 may be conserved in colorectal cancer and glioma cells. TCF4 may be involved in a series of important biological processes such as regulation of metabolic and biosynthetic (GO: 0010604, GO: 0031328, GO: 0009891, GO: 0051173, GO: 0010557, GO: 0045935), adhesion (GO: 0007155, GO: 0022610), apoptosis (GO: 0042981, GO: 0043067, GO: 0010941), and important signaling pathways (Wnt, Chemokine, Calciu, GnRH).
authors.affiliation: Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University 268 Kaixuan Road, Hangzhou 310029, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Chen
authors.affiliation: Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University 268 Kaixuan Road, Hangzhou 310029, China.
authors.forename: Yachun
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University 268 Kaixuan Road, Hangzhou 310029, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
authors.affiliation: Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University 268 Kaixuan Road, Hangzhou 310029, China.
authors.forename: Lisha
authors.initials: L
authors.lastname: Li
authors.affiliation: Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University 268 Kaixuan Road, Hangzhou 310029, China.
authors.forename: Na
authors.initials: N
authors.lastname: Zhao
authors.affiliation: Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University 268 Kaixuan Road, Hangzhou 310029, China ; Swedish Medical Center Seattle, WA 98122, USA ; Department of Urology, University of Washington Seattle, WA 98195, USA.
authors.forename: Biaoyang
authors.initials: B
authors.lastname: Lin
keywords: ChIP-seq; TCF4; Wnt signaling pathway; colorectal cancer