GSE127183
Genome wide mapping of binding sites of the EMT-inducing transcription factor SNAIL1 in LS174T colorectal cancer cells
At the molecular level, epithelial-to-mesenchymal transition (EMT) necessitates extensive transcriptional reprogramming which is orchestrated by a small group of gene regulatory proteins. The transcription factor SNAIL1 is a zinc-finger DNA-binding protein and well-known master regulator of EMT. However, knowledge of its immediate target genes is incomplete. Here, we performed ChIP-seq to chart genome-wide SNAIL1 chromosomal binding sites and to identify genes directly regulated by SNAIL1. For this we used the colorectal adenocarcinoma cell line LS174T which was engineered to express hemagglutinin epitope-tagged murine SNAIL1 in a doxycycline inducible fashion. In total, 1501 SNAIL1-HA ChIP-seq peaks were mapped which were linked to 1307 genes based on nearest neighbor relationships. The vast majority of SNAIL1-HA binding events occurred within 1 kb upstream of transcriptional start sites (44%), and in intergenic regions and promoter-distal introns (46%). De novo motif deduction showed that nearly all ChIP-seq peak regions harbored at least one sequence element corresponding to the cognate SNAIL1 DNA-recognition motif 5'-CAGGTG-3'. SNAIL1-HA ChIP-seq peaks included previously determined SNAIL1 binding sites at the FOXA1, EPHB3, ITGB4 and CLDN3 genes, thus validating the ChIP-Seq results. When comparing the genomic distribution of SNAIL1-HA to that of the intestinal stem cell (ISC) transcription factors ASCL2 and TCF7L2, we observed a significant overlap. Furthermore, SNAIL1-HA ChIP-seq peaks are associated with a substantial fraction of ISC signature genes. In two colorectal cancer cell lines, we verified that SNAIL1 decreases ISC marker expression. Likewise, SNAIL1-HA  was found to occupy multiple regulatory elements at the proto-oncogene MYB, and the long non-coding RNA (lncRNA) WiNTRLINC1, a recently described regulator of ASCL2. Occupancy of the MYB and WiNTRLINC1 regulatory elements by SNAIL1-HA correlated with the downregulation of the two genes. We propose that SNAIL1-mediated repression of MYB and ISC markers like WiNTRLINC1 contributes to the decrease in proliferation known to be associated with EMT, while simultaneously abrogating stemness features of colorectal cancer cells. Overall design: SNAIL1 chromosomal binding profiles were obtained by chromatin immunoprecipitation followed by next generation sequencing from LS174T colorectal cancer cells allowing for doxycycline-inducible expression of hemagglutinine epitope-tagged murine SNAIL1. Two biological replicates of uninduced (control) and induced (SNAIL1-HA expressing) cells were analyzed. DNA isolated from chromatin not subjected to immunoprecipitation (Input) was sequenced as reference material.