Selective redistribution of RNA Pol II in response to osmostress. (a) Comparison of gene expression changes from microarray data on wild-type (wt) cells subjected to osmostress (0.4 M NaCl, 15 minutes; see Materials and methods; Additional file 2). Bars represent the mean fold change for osmoresponsive ORFs with fold change > 1.75 upon osmostress (662 genes) and total ORFs present in the array except those considered osmoresponsive (5,655 genes; see Materials and methods). (b) A scatter plot showing RNA Pol II occupancy in basal conditions (YPD; x-axis) versus osmostress (0.4 M NaCl, 10 minutes; y-axis). Each dot represents normalized hits (TRPK; trimmed mean of M values normalized read/kilobase density). Black dots and the trend line represent TRPK distribution of total ORFs in the genome except osmoresponsive genes. Osmoresponsive genes are represented as red dots. (c) RNA Pol II binding kinetics to osmoresponsive and constitutively expressed genes. Left-hand panels: association of RNA Pol II upon osmostress (0.4 M NaCl, for the indicated times) was assessed by ChIP to STL1 osmoresponsive gene and PMA1. Real-time quantitative PCR (qPCR) results are shown as fold induction of treated versus non-treated (time zero). Right-hand panels: overlapping ChIP-Seq tracks representing RNA Pol II normalized hits at the STL1 and PMA1 loci in the presence (red histogram) or in the absence (black histogram) of osmostress. Red and black histograms have been overlaid. The blue arrow indicates annotated ORF. (d) Role of Hog1 in RNA Pol II recruitment. MA plots of RNA Pol II binding in wild-type upon osmostress (left-hand panel; see Materials and methods). MA plots of RNA Pol II binding wild-type versus hog1 mutant stressed as before. The dotted red line delimits the threshold for significance (P = 0.0001). Highlighted dots indicate a subset of 100 osmoresponsive genes that are differentially expressed based on the dependency of the SAPK (Hog1-dependent in green and Hog1-independent in red).
Nadal-Ribelles et al. Genome Biology 2012 13:R106 doi:10.1186/gb-2012-13-11-r106