Swapping of upstream regulatory sequences affects transcription and mRNA degradation. (a) Scheme describing the generation of S. cerevisiae Swap strains by replacing the native S. cerevisiae promoter and 5' UTR with the orthologous sequences from S. paradoxus. Note that for each strain we modulate the regulatory region of only one gene while all other loci are identical to the wild-type (WT) S. cerevisiae. (b) Log2-ratio of mRNA levels in the swapped versus WT strains are shown for 34 genes with a predicted cis-dependent interspecies expression difference. Colors represent the concordance between the swapping effect and the inter-species expression difference. Expression changes of less than 40% were considered not significant, as the interspecies expression differences were approximately two-fold. (c) Log2-ratio of mRNA levels in the Swapped versus WT strains after transcriptional arrest. Colors indicate whether mRNA degradation rates are increased (red), decreased (green) or not significantly affected (black, P > 0.05). The average values from three technical replicates are shown along with regression lines. Error bars show standard deviation among three technical replicates, while both values are shown for experiments with two biological replicates (AAT2, MKC7, OXP1 and YML108W). (d) Same as (c) for a validation experiment of four selected genes with eight time points.
Dori-Bachash et al. Genome Biology 2012 13:R114 doi:10.1186/gb-2012-13-12-r114