Analysis of the repressive activity of RBPJ in a mature T cell line

The Notch signaling pathway regulates gene expression via the transcription factor RBPJ. Here we investigated the the repressive role of RBPJ in a mature T cell line by combining RNA-Seq, ChIP-Seq and ATAC-Seq data under several different conditions. Overall design: Mouse mature T cells were analyzed by ChIP-Seq using an RBPJ-specific antibody upon RBPJ depletion or Notch activation. In addition, histone modifications such as H3K27ac, H3K4me1 and H3K4me3 were analyzed together with chromatin accessibility (ATAC-Seq) upon RBPJ depletion. Finally, gene expression was analyzed upon RBPJ depletion, Notch induction, gamma-secretase inhibitor (GSI) DAPT treatment, by overexpressing the active Notch intracellular domain (NICD) in the RBPJ depleted background or overexpression the RBPJ interactor KYOT2.