Figure 2.

PHB overexpression downregulates genes involved in S-phase progression. (a) Histogram of RNA-seq reads of PHB mRNA transcript fragments from LNCaP/PHB^cDNA cells±doxycycline for 16 h overlayed on the gene structure of PHB (RefSeq, 2016)—indicating the doxycycline-induced overexpression of PHB RNA fragments (from integrated plasmid). (b) Diagram showing the hierarchical clustering analysis of the 2000+ genes either upregulated or downregulated from LNCaP/PHB^cDNA cells±doxycycline (∓2-fold, P⩽0.05). Drawn in the Partek software, blue indicates gene downregulation, and red gene upregulation. (c) Bar charts indicating the most significant cellular processes (left-hand side) and gene networks (right-hand side) influenced by PHB overexpression. Produced in the Metacore software from a list of genes (2000)∓2-fold, P⩽0.05. (d) Table listing the cellular networks associated with the gene expression changes in LNCaP/PHB^cDNA cells±doxycycline, summary from the IPA (Igenuity) and DAVID software. (e–h) Q-PCR validation of genes found to be involved in S-phase progression (e), in checkpoint activation (f), in DNA replication and AR responsiveness (g) and housekeeping genes (h). All data are the mean±s.d. of three independent experiments performed in triplicate. *P<0.05 and **P<0.01 (t-test analysis).