Genome-wide localisation analysis for IRF4 target gene identification in melanoma cell lines

Interferon Regulatory Factor 4 (IRF4) is a key transcription factor in development and function of immune cells. Also it has been shown that elevated IRF4 expression is a key factor for survival in some myeloid and lymphoid cancers. Recently, studies have shown IRF4 expression also in non-immune cells and malignancies such as melanocytes and melanoma. Studies from our lab and elsewhere demonstrated elevated expression levels of IRF4 is critical for melanocytes and melanoma cell lines. There is lack of knowledge about IRF4 regulated genes in melanoma, so we aimed at identification of its localization genome-wide using high-throughput sequencing of immunoprecipitated chromatin (ChIP-seq). First, we established and optimized ChIP-qPCR (Chromatin immunoprecipitation coupled with quantitative polymerase chain reaction) experiments in our lab and confirmed several IRF4 binding regions in different loci such as Tyrosinase, a key developmental gene in melanocytes. Then, we performed ChIP-seq to identify IRF4 target genes genome-wide in a melanoma cell line. We set up a bioinformatics pipeline and analysed the ChIP-seq data to find putative IRF4 binding regions and their associated genes. Afterwards, we characterized DNA motifs,associated genes, pathways and biological processes. Our results integrated with previous RNA-seq data suggests that IRF4 is regulating genes related to cell cycle and proliferation, and in cellular transport system.