Supplemental Data Set 2. Analysis of NMD Target Features for All Events.

(A) General information on mapping of all and the significantly changed alternative splicing events.
(B) AS event positions relative to the cds of the representative transcript model annotated in TAIR10 for all AS events and those significantly changed in the different samples. Subsets as described in Figure 3B.
(C) Analysis of NMD target feature frequencies for the AS events significantly changed in the indicated samples. For each AS event and dependent on the direction of the AS ratio change, one of the two corresponding splicing variants was assigned to the control sample (WT or Mock treatment), whereas the other was assigned to the NMD-impaired sample (“Δ NMD”). This splicing variant assignment then allowed counting how many of those contained classical NMD features, separately analyzing events mapping to the 5’ UTR, cds, and 3’ UTR. NMD feature inspection included upstream open reading frames (uORFs), translation initiation site (TIS) overlapping uORFs, occurrence of PTCs leading to 3’ UTRs > 347 nts, splice junctions more than 50 nts downstream of a stop codon, and PTC-independent, long 3’ UTRs > 347 nts.
(D) Frequency patterns of NMD-eliciting features in different datasets. Occurrence of NMD features described in (C) were analyzed considering the following categories: splicing variant assigned to the control, but not to the NMD impairment has NMD feature (1,0), splicing variant assigned to the NMD impairment, but not to the control has NMD feature (0,1), both splicing variants have NMD feature (1,1), and none splicing variant has NMD feature (0,0).
(E) 3’ UTR length distribution for transcripts assigned to the control or NMD-impaired samples for the indicated subsets. Assignments of two splicing variants for each event as described in (C).
(F) 5’ UTR length distribution for transcripts assigned to the control or NMD-impaired samples for the indicated subsets. Assignments of two splicing variants for each event as described in (C).
(G) Numbers of genes containing single or multiple significantly changed AS events for the indicated subsets. For the genes with multiple events, transcripts with all possible combinations were assembled and analyzed for the rescue of a PTC introduced by a single event.
Further details on data analysis are provided in Supplemental Methods.