Genomic Run On (GRO): determination of the nascent transcriptional rate and mRNA amount during alkaline stress response

We study the transcriptional response of wt S. cerevisiae cells to alkaline pH by using a genome-wide method (Genomic run-on) that allows for the determination of transcription rates (TR) and mRNA amounts (RA) for each gene. The stabilities of the mRNAs can be calculated from the TR and RA data. S. cerevisiae cells grown in YPD pH 5.5 to exponential phase and transfered for the indicated times to pH 8, at each time aliquots were subjected to Genomic Run On. Conventional mRNA levels were obtained from cDNA labelling on the same array. Home-made microarrays containing 6035 ORF were used. Three replicates of the experiment were done.