Figure 3.

Stress-induced cryptic transcripts are repressed by INO80. Properties of stress induced cryptic transcripts induced by osmotic stress (0.4M NaCl) ientified by genome survey. (A) Example transcript maps for SITs. RNA signal intensities for both strands (W and C) are shown for the different profiled samples (y-axis): annotated ORFs are indicated as blue boxes and SITs as orange boxes. Transcription orientation and intensity are indicated by green arrows. SIT37 and SIT30 are antisense oriented, SIT6 is downstream of AAC3, and SIT31 and SIT129 are originating from bidirectional promoters. (B) Nucleosome eviction at SITs is similar to canonical genes. Median nucleosome occupancy is reduced at SIT transcript start sites after treatment with hyperosmotic stress in wild-type cells and arp8Δ cells but nucleosome eviction (shown as nucleosome difference, right panel) persists in arp8Δ cells. (C) Mutants lacking Arp8 have prolonged SIT expression shown here as median expression change (log₂) wild-type (blue) and arp8Δ (orange). (D) Eviction at strong promoters is bidirectional and enhanced in arp8Δ cells. The left panel shows nucleosome density maps of the bidirectional transcripts of the 56 most highly activated stress-induced loci. The right panel shows the median nucleosome occupancy in wild-type and arp8Δ of the selected genes. (E) Median expression differences of 5΄ opposing strand transcripts compared to gene transcripts.