Transcriptomics,Genomics

Dataset Information

22

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


ABSTRACT: 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. 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).

INSTRUMENT(S): Illumina Genome Analyzer II (Trypanosoma brucei)

SUBMITTER: Daniel Nilsson   

PROVIDER: GSE22571 | GEO | 2010-06-25

SECONDARY ACCESSION(S): PRJNA128439

REPOSITORIES: GEO

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Publications

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

Nilsson Daniel D   Gunasekera Kapila K   Mani Jan J   Osteras Magne M   Farinelli Laurent L   Baerlocher Loic L   Roditi Isabel I   Ochsenreiter Torsten T  

PLoS pathogens 20100805 8


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 blo  ...[more]

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