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.
Cover
IFC
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
IBC
BC
Zoom level
fit page
fit width
A
A
fullscreen
one page
two pages
print
SlideShow
fullscreen
in this issue
search
back issues
help
Open Article
Open Article
Close Article
article text for page
< previous story
|
next story >
Share this page with a friend
Save to “My Stuff”
Subscribe to this magazine
Search
Help