Dataset Information

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 ?-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.

Conclusion

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).

SUBMITTER: Chen C

PROVIDER: S-EPMC4276198 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

Genome-wide ChIP-seq analysis of TCF4 binding regions in colorectal cancer cells.

Chen Chen C Lu Yachun Y Liu Jie J Li Lisha L Zhao Na N Lin Biaoyang B

International journal of clinical and experimental medicine 20141115 11

<h4>Objective</h4>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.<h4>Methods</h4>SW620 human colorectal cancer cells were cultured. The TCF ...[more]

PMID: 25550940

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Project description:ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with ultra high-throughput massively parallel sequencing, is increasingly being used for mapping protein-DNA interactions in-vivo on a genome scale. Typically, short sequence reads from ChIP-Seq are mapped to a reference genome for further analysis. Although genomic regions enriched with mapped reads could be inferred as approximate binding regions, short read lengths (approximately 25-50 nt) pose challenges for determining the exact binding sites within these regions. Here, we present SISSRs (Site Identification from Short Sequence Reads), a novel algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. The sensitivity and specificity of SISSRs are demonstrated by applying it on ChIP-Seq data for three widely studied and well-characterized human transcription factors: CTCF (CCCTC-binding factor), NRSF (neuron-restrictive silencer factor) and STAT1 (signal transducer and activator of transcription protein 1). We identified 26 814, 5813 and 73 956 binding sites for CTCF, NRSF and STAT1 proteins, respectively, which is 32, 299 and 78% more than that inferred previously for the respective proteins. Motif analysis revealed that an overwhelming majority of the identified binding sites contained the previously established consensus binding sequence for the respective proteins, thus attesting for SISSRs' accuracy. SISSRs' sensitivity and precision facilitated further analyses of ChIP-Seq data revealing interesting insights, which we believe will serve as guidance for designing ChIP-Seq experiments to map in vivo protein-DNA interactions. We also show that tag densities at the binding sites are a good indicator of protein-DNA binding affinity, which could be used to distinguish and characterize strong and weak binding sites. Using tag density as an indicator of DNA-binding affinity, we have identified core residues within the NRSF and CTCF binding sites that are critical for a stronger DNA binding.

Dataset Information

Genome-wide ChIP-seq analysis of TCF4 binding regions in colorectal cancer cells.

Objective

Methods

Results

Conclusion

Publications

Genome-wide ChIP-seq analysis of TCF4 binding regions in colorectal cancer cells.

Similar Datasets

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