Figure 3

Identification of UPF1, EXOSC5 and STAU1 as factors controlling RNA half-lives. (a–c) ChIP-seq and RNA-seq for the GADD45A (a), FAM120C (d) and CDKN2B (c) genes, which showed significant changes in RNA half-lives in UPF1, EXOSC5 and STAU1 knocked-down cells, respectively. Upper two panels in (a–c): ChIP-seq data for H3K4me3 and pol II. Lower two panels in (a–c): RNA-seq data for control cells and the respective knockdown cells. (d–f) BRIC-seq normalized graph for GADD45A (d), FAM120C (e) and CDKN2B (f) genes in control cells or cells knocked-down for UPF1 (d), EXOSC5 (e), and STAU1 (f). (g) Scatterplot representing the ChIP-seq peak signal intensities of H3K4me3 on the y-axis and gene expression values on the x-axis with putative UPF1-controlled genes, EXOSC5-controlled and STAU1-controlled genes in blue, green and red dots respectively.