Coupled evolution of transcription and mRNA degradation.

We measured mRNA levels of two yeast species (S.cerevisiae and S.paradoxus) and their hybrid, at four time-points (0, 20min, 40min, 60min) following transcription arrest using 1,10-Phenantroline (150ug/ml). This data was used to infer mRNA degradation rates of orthologous genes, study the divergence of mRNA degradation rates and the contribution of cis and trans mutations. For each of the two biological repeats and each of the four time point, poly(A) mRNAs of the two species was pooled and labeled with cy3 while hybrid poly(A) mRNA was labeled with cy5 and these were hybridized to our custom two-species microarray (Agilent) with four subarrays.