Signal-Specific Genomic Regulation of NF-?B by EGFR and IL-1R

To study how NF-?B-dependent transcription is regulated differentially by EGFR, compared to the Interleukin-1 receptor (IL-1R), a classical NF-?B activator, we integrated transcriptional analyses by profiling by RNA-seq) and DNA binding by ChIP-seq analyses in human mammary epithelial cells (HMECs). Overall design: Signal-specific NF-?B-dependent genes activated or repressed by EGF or IL-1 were identified by differential gene expression analysis of RNA-seq data of treated versus untreated samples with or without knockdown of the RELA (p65) subunit of NF-?B. Signal-specific NF-?B binding sites were identified by ChIP-seq using an antibody against p65 followed by differential binding analysis of p65 peaks in treated versus untreated samples.