Transcript-averaged PAR-CLIP occupancy profiles are shown for RNA degradation factors involved in (
A) deadenylation, (
B) decapping, (
C) 5´→3´ exonuclease Xrn1, (
D) exosome, (
E) TRAMP, (
F) Ski, and (
G) NMD. Transcripts are aligned either at transcript start site (TSS) and poly-adenylation (pA) site (marked with blue) or at their start and stop codons (marked with green). TIF-seq based annotation is shown in blue (n = 3193 for TSS and pA site profiles) (
Pelechano et al., 2013). Open reading frames (ORF) annotated in the SGD (version 64.2.1) are shown in green (n = 4012 for TSS, and n = 3965 for pA site selected transcripts). To avoid contaminating signals from neighboring genes, we filtered out regions that had annotations upstream and downstream of the centered gene (up to 700 nt) (Materials and methods). Shaded areas (in blue TIF-seq annotation, or in green for ORF annotation) depict 95% confidence intervals derived from bootstrapping genes. Comparison between these two profiles highlights preferences for end binding degradation factors in binding to untranslated regions at the two sides of the transcript.