  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/.
