title: Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei.
abstract: Trans-splicing of leader sequences onto the 5'ends of mRNAs is a widespread phenomenon in protozoa, nematodes and some chordates. Using parallel sequencing we have developed a method to simultaneously map 5'splice 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 5' 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/.
authors.affiliation: Institute of Cell Biology, University of Bern, Bern, Switzerland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Nilsson
authors.forename: Kapila
authors.initials: K
authors.lastname: Gunasekera
authors.forename: Jan
authors.initials: J
authors.lastname: Mani
authors.forename: Magne
authors.initials: M
authors.lastname: Osteras
authors.forename: Laurent
authors.initials: L
authors.lastname: Farinelli
authors.forename: Loic
authors.initials: L
authors.lastname: Baerlocher
authors.forename: Isabel
authors.initials: I
authors.lastname: Roditi
authors.forename: Torsten
authors.initials: T
authors.lastname: Ochsenreiter
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D017398:Alternative Splicing / Q000235:genetics*; D001483:Base Sequence; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D017125:Genes, Protozoan / Q000235:genetics*; D008969:Molecular Sequence Data; D012333:RNA, Messenger / Q000235:genetics; D020038:RNA, Spliced Leader / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014346:Trypanosoma brucei brucei / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D012333:RNA, Messenger; D020038:RNA, Spliced Leader