Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ChIP-exo)
Transcription factor binding to DNA is a central mechanism regulating cellular gene expression. Thus, thorough characterization of this process is essential for understanding cellular biology in both health and disease. In this study, we combined data from three sequencing-based methods to unravel the DNA binding function of the novel zinc finger protein ZNF414 in cells representing two tumor types. ChIP-exo served to map protein binding sites in the genome, ATAC-seq allowed identification of open chromatin, and RNA-seq examined the transcriptome. Overall design: We characterized ZNF414 DNA binding in human pancreatic tumor cell line Hs700T and in human breast cancer cell line MCF-7 using ChIP-exo with an antibody against V5 tag. Cells were transfected with pcDNA6.2/EmGFP-Bsd/V5-DEST-ZNF414 plasmid for overexpression of V5-tagged ZNF414 48 hours before sample collection and two biological replicates were used per cell line.