Science Magazine - 2 November 2012

Fig. 2. Ssu72 inactivation leads to ncRNA tran-
scription (SRTs). (A) I to IV: Genomic transcrip-
tion across 28 kilobases of chromosomes 2 and 4 (x axis) for the Watson (W, top) and the Crick (C, bottom) strands.Fo r the whole genome, see http://
steinmetzlab.embl.de/proudfoot_lab/index.html. Normalized signal intensities are shown for profiled samples (y axis). Triplicate data are shown for the wild type
(1 to 3), ssu72-2 (1 to 3), Drrp6 (1 to 3), and ssu72-2Drrp6 (1 to 3) strains. Red vertical lines represent inferred transcript boundaries. Nucleosome positions
[green tracks (darker for higher occupancy) (25) and genome annotations are shown in the center: annotated ORFs (blue boxes), ncRNAs (orange boxes), and
TSSs (arrows)]. (I) ncRNA0151, (II) ncRNA0397, (III) ncRNA0524, and (IV) ncRNA4353 represent promoter-associated SRTs. (B) Distribution of relative distances
of 605 SRTs (upper panel) versus 1982 CUTs (lower panel) to their nearest ORF TSS (red line). Dashed lines (350 bp) indicate the cut-off position used to define
intergenic cryptic transcription–sharing ORF promoters. (C) Distributions of gene expression levels are shown for downstream (down) and upstream (up) ORFs of
tandem genes [three categories: downstream promoter pSRT (blue), pCUT (purple), or no pncRNA (green)]. Downstream ORFs with pncRNAs are significantly
higher expressed than those without (P = 0.001 [pSRT] and P < 2.2 × 10–16 [pCUTs]). No significant association was found for upstream ORFs. (D) Pol II profiles
for ssu72-2 (red) and the wild type (blue) around the ORF promoter in tandem genes that are more than 400 bp apart. Solid lines indicate median Pol II
occupancy; shaded areas denote 25 to 75 percentiles. Pol II occupancy increases upstream of TSSs in ssu72-2.

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