RNA synthesis precision is regulated by preinitiation complex turnover

Global changes in RNA length in mot1-42 and set2Δ cells. (A) Integrated Genome Browser (Nicol et al. 2009) screen shot of log₂ RNA profiles in WT (black) and mot1-42 (red) cells. The differential RNA profile (log₂ mot1-42/WT) is shown in the blue track. Annotated genes are in green, with positions above or below the chromosomal coordinate indicating whether the genes are transcribed on the top or bottom strand. The short black and red horizontal bars denote RNA length changes captured by the method, as illustrated more clearly in panel B. (B) Overview of the method, illustrated with an enlargement of the chromosomal region in the center of the screen shot in A. In the case of the gene YBR284W, the significant differential RNA segment found using signal log₂(mot1-42/WT) > 0.3 (blue segment) was compared with the annotation, and aberrant transcript length changes (denoted by the red and the black segments) were calculated. Thresholds requiring a ≥100 bp overlapping gene segment and length changes ≥150 bp long were applied. S_overlap and S_ext refer to the differential RNA signal in the region where the differential segment overlaps (orange segment) and is external (black segment) to the annotation, respectively. S_int refers to the differential signal within the portion of the annotation that does not overlap the differential segment (red segment). By provisionally defining the differential RNA with respect to the overlapping gene, the aberrant RNAs were sorted among four groups (see text). In this example, a 5′ length change is classified as an upstream initiation event, whereas the partial overlapping gene segment and consequent change in 3′ length define a premature termination event. Although this example shows, for illustrative purposes, a gene with two types of RNA length changes, most of the genes with length changes in mot1-42 cells (92.4%) displayed only a single type as indicated in the table in panel C. (C) The table summarizes the number of aberrant RNAs identified from the differential RNA signal as in B in mot1-42 and set2Δ cells compared with WT cells. Of particular note is the large number of premature termination events in mot1-42 cells and the enrichment in downstream (cryptic) initiation events in set2Δ cells.