Fig. 3: Identification of thousands of regulatory 3’-UTRs.
From: Post-transcriptional reprogramming by thousands of mRNA untranslated regions in trypanosomes
a The violin plot shows relative enrichment of inter-CDS fragments cloned in their native or inverted orientation. Blasticidin selection for positive control; green, n = 1941 fragments. Ganciclovir selection for negative control; magenta, n = 2282 fragments. The open circles indicate median values, while t-tests were two-sided. b 3’-UTR associated fragments were ranked based on indexed read fold-change between the positive and negative selection screens. Previously published regulatory 3’-UTRs (see Supplementary Data 1) that feature as hits are highlighted. c The maps show UTR-seq read-density for two exemplar positive regulatory 3’-UTR fragments. Sense paired, indexed reads are indicated by the green lines, with total reads indicated in grey. UTR hit fragments are indicated as green boxes; with arrows indicating direction of transcription from left to right. RNA-seq (solid green) and ribosome profiling data (black) are also shown. The upper protein-map shows the relationship between the paralogs (PGKB-C) with identical amino acids shown in white, different amino acids in grey and additional segments in one of the proteins in black. d The maps show read-density for two exemplar negative regulatory 3’-UTRs. Sense indexed reads are indicated by the magenta line and UTR hit fragments are indicated as magenta boxed arrows. The paralogs compared in this case are NT8.1-2. Other details as for (c). e The map shows read-density for the hexose transporter locus with both positive and negative regulatory 3’-UTR fragments. Other details as for (c, d). f The boxplot shows length data for putative positive (n = 844) and negative (n = 468) regulatory 3’-UTRs associated with hit fragments that also include downstream mRNA processing sequences. Boxes indicate the interquartile range (IQR), the whiskers show the range of values within 1.5*IQR and a horizontal line indicates the median. The notches represent the 95% confidence interval for each median. The t-test was two-sided.
