Fig. 5: Non-canonical splicing activity in Ulcerative colitis patients.

(a) Quantification of de novo junctions in healthy donors (Cont, n = 20) and in UC patients (n = 206) from the PROTECT UC cohort RNA-seq data (GSE109142). De novo junctions were defined as junctions not annotated in the hg19 version of the human genome and not present in both healthy donors and UC patients. Values shown were normalized by the total number of reads in each RNA-seq experiment to account to eventual variations in the depth of the sequencing. P Value was calculated with an unpaired two-sided Student’s t test. Boxplot center indicates the median, the (x) indicates the mean, bounds of the box indicate the 1st and 3rd quartiles, lower and upper whiskers define minima and maxima. When outliers are present, whiskers instead extend 1.5 times the interquartile range. Outliers are shown as dot. (b) String chart representing the normalized de novo junction count for each donor (healthy in blue, UC patients in red). Framed areas represent approximately the patients included in the indicated quartiles. (c) Genes differentially expressed (>1.5-fold, P Val < 0.01) between patients in the lower and the upper quartiles were compared to Gene Ontology annotations. Pathways significantly (P val < 0.01) enriched in the category of “biological processes” are indicated. (d) De novo junctions were quantified at genes that, transcriptionally, were affected <1.5-fold between healthy donors and UC patients. For each indicated condition, we counted genes gaining de novo junction 1.5-fold or more (p Val < 0.01). (e) Splice junctions in a representative healthy donor and a representative UC patient were visualized with a genome browser in the neighborhood of the LMNA gene (indicated in red). Each bar represents a donor/acceptor couple, spanning from the 5′ to the 3′ splice site. The histograms in the top tracks represent the local read density in the RNA-seq data. The UC patient was chosen in the upper quartile but does not display the highest de novo junction count (f–h) Taqman Assays lamin A and progerin in control (n = 17), Crohn disease (CD, n = 16) and Ulcerative colitis (UC, n = 19) populations, cDNA were extracted from colon biopsies. Mann–Witney U test. (h) example of sequencing data from the Taqman PCR end products in one UC patient, Human fibroblast from HGPS patient was used as positive control, UC = Ulcerative colitis. Source data are provided as a Source Data file.