Spliced Leader Trapping Reveals Widespread Alternative Splicing Patterns in the Highly Dynamic Transcriptome of Trypanosoma brucei

TL;DR

This study introduces a new sequencing-based method called spliced leader trapping (SLT) to map trans-splicing sites and analyze gene expression in Trypanosoma brucei, revealing extensive alternative splicing and stage-specific regulation.

Contribution

The paper presents SLT, a novel method for mapping trans-splice sites and analyzing transcriptomes, uncovering widespread alternative splicing in T. brucei.

Findings

Detected 85% of annotated genes' splice sites

Found up to 40% of transcripts differentially expressed

Discovered over 2500 stage-regulated alternative splicing events

Abstract

Trans-splicing of leader sequences onto the 59ends of mRNAs is a widespread phenomenon in protozoa, nematodes and some chordates. Using parallel sequencing we have developed a method to simultaneously map 59splice sites and analyze the corresponding gene expression profile, that we term spliced leader trapping (SLT). The method can be applied to any organism with a sequenced genome and trans-splicing of a conserved leader sequence. We analyzed the expression profiles and splicing patterns of bloodstream and insect forms of the parasite Trypanosoma brucei. We detected the 59splice sites of 85% of the annotated protein-coding genes and, contrary to previous reports, found up to 40% of transcripts to be differentially expressed. Furthermore, we discovered more than 2500 alternative splicing events, many of which appear to be stage-regulated. Based on our findings we hypothesize that alternatively spliced transcripts present a new means of regulating gene expression and could potentially contribute to protein diversity in the parasite. The entire dataset can be accessed online at TriTrypDB or through: http://splicer.unibe.ch/.