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| Status |
Public on Jun 25, 2010 |
| Title |
Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei |
| Organism |
Trypanosoma brucei |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Some organisms like the human and animal parasite Trypanosoma brucei add a leader sequence to their mRNAs through a reaction called trans-splicing. Until now the splice sites for most mRNAs were unknown in T. brucei. Using high throughput sequencing we have developed a method to identify the splice sites and at the same time measure the abundance of the corresponding mRNAs. Analyzing three different life cycle stages of the parasite we identified the vast majority of splice sites in the organism and, to our great surprise, uncovered more than 2500 alternative splicing events, many of which appeared to be specific for one of the life cycle stages. Alternative splicing is a result of the addition of the leader sequence to different positions on the mRNA, leading to mixed mRNA populations that can encode for proteins with varying properties. One of the most obvious changes caused by alternative splicing is the gain or loss of targeting signals, leading to differential localization of the corresponding proteins. Based on our findings we hypothesize that alternative splicing is a major mechanism to regulate gene expression in T. brucei and could contribute to protein diversity in the parasite.
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| Overall design |
In total we sequenced three libraries from bloodstream form mRNA, (long slender and short stumpy, both Antat1.1 and monomorphic Lister 427), one from procyclic form mRNA (Antat1.1), 2x2 RNAi libraries (uninduced and induced), where each pair could be considered a biological replicate. Lastly we prepared and sequenced one conventional RNAseq library from procyclic mRNA (Antat1.1).
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| Contributor(s) |
Nilsson D, Gunasekera K, Mani J, Osteras M, Farinelli L, Baerlocher L, Roditi I, Ochsenreiter T |
| Citation(s) |
20700444 |
| |
| Submission date |
Jun 25, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Nilsson |
| E-mail(s) |
daniel.nilsson@izb.unibe.ch
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| URL |
http://splicer.unibe.ch
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| Organization name |
University of Bern
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| Department |
Institute of Cell Biology
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| Street address |
Baltzerstrasse 4
|
| City |
Bern |
| ZIP/Postal code |
3012 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL10599 |
Illumina Genome Analyzer II (Trypanosoma brucei) |
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| Samples (9)
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| Relations |
| SRA |
SRP002776 |
| BioProject |
PRJNA128439 |
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