Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei

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 59 splice 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/. © 2010 nilsson et al.