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 (RNA-seq)

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. We characterized the effect of ZNF414 expression on genomewide gene expression levels in human pancreatic cell line Hs700T and in human breast cancer cell line MCF-7. For this, we silenced ZNF414 gene by siRNA transfection in these cells and performed RNA-seq on transfected and control (Luciferase siRNA-transfected) cells at 12h and 24h timepoints.