Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei.
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/.
Nilsson
Daniel
D
Institute of Cell Biology, University of Bern, Bern, Switzerland.
Gunasekera
Kapila
K
Mani
Jan
J
Osteras
Magne
M
Farinelli
Laurent
L
Baerlocher
Loic
L
Roditi
Isabel
I
Ochsenreiter
Torsten
T
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*
D020121:5' Untranslated Regions; D012333:RNA, Messenger; D020038:RNA, Spliced Leader