PMC

Conservation of the presence and regulation of antisense units in Hemiascomycota. Shown are the differential expression values of antisense and sense units comparing mid-log and early stationary phase across S. cerevisiae and the five other species (red, higher in early stationary phase; green, lower in early stationary phase; black, no change; hatched, no candidate orthologous contig; grey, no antisense transcription detected in species). A phylogenetic tree of the species included in this study [] is shown above (the star indicates the WGD).

Effect of Rrp6 and Hda2 on antisense transcript levels and sense-antisense regulation. (a,b) The distribution of changes in expression levels (x-axis) for sense (blue) and antisense (orange) transcripts in the Δrrp6 (a) and Δhda2 (b) mutants compared to the wild type (wt). In the Δrrp6 mutant (a) there is a mild increase in antisense levels and decrease in sense levels. No such changes are observed in the Δhda2 mutant (b). (c) Negative correlation between change in antisense transcript (y-axis) and in sense transcript (x-axis) in the Δrrp6 mutant relative to the wild-type strain. (d) Similarity in differential sense gene expression from mid-log to early stationary phase between the wild type (x-axis) and the Δrrp6 mutant (y-axis).

Strand-specific RNA-seq identifies 1,103 antisense units associated with stationary phase, stress, and meiosis genes in S. cerevisiae. (a) Typical short antisense (Unit3689, antisense to NOP10). Shown are reads mapped from a standard cDNA sequencing library [] (yellow), and from the strand-specific library prepared and run side-by-side on the same flow cell (green: forward reads above, reverse reads below). All coverage tracks were normalized to the total number of reads mapped, and are shown up to a threshold of 3 × 10^-8 of total mapped reads (genome-wide). Units were called from the strand-specific library (blue units, known genes; orange, putative antisense), and are shown along with the manually curated units (red) and the known gene annotations from the SGD (gray). (b) Typical long antisense (ManualUnit225, antisense to MBR1). Tracks are as in (a). The figures are shown using the Integrative Genome Viewer [].

Quantitative expression measurements of putative antisense units and the corresponding sense genes in S. cerevisiae. (a) Strand-specific qRT-PCR measurements of six pairs of known sense genes and their putative antisense units in comparing mid-log and early stationary phase (the y-axis shows the log₂ ratio of expression in early stationary phase versus mid-log). Error bars indicate the standard deviation between biological replicates and different primers. (b) nCounter [] measurements of nine representative putative antisense units, comparing mid-log to early stationary phase, stationary phase, heat shock and salt stress (the y-axis is as in (a) for the examined condition). Error bars indicate the standard deviation between biological replicates. (c) nCounter measurement for 67 tested sense-antisense pairs in early stationary phase (left) and heat shock (right), each relative to a mid-log (no stress) control. The columns marked 'S' and 'A' represent the sense and antisense change, respectively. Red, induced; green, repressed; black, no change. The names of genes highlighted in the main text are shown in red.