RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs

Shulamit Michaeli, Tirza Doniger, Sachin Kumar Gupta, Omri Wurtzel, Mali Romano, Damian Visnovezky, Rotem Sorek, Ron Unger, Elisabetta Ullu

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31 Scopus citations


The discovery of a plethora of small non-coding RNAs (ncRNAs) has fundamentally changed our understanding of how genes are regulated. In this study, we employed the power of deep sequencing of RNA (RNA-seq) to examine the repertoire of ncRNAs present in small ribonucleoprotein particles (RNPs) of Trypanosoma brucei, an important protozoan parasite. We identified new C/D and H/ACA small nucleolar RNAs (snoRNAs), as well as tens of putative novel non-coding RNAs; several of these are processed from trans-spliced and polyadenylated transcripts. The RNA-seq analysis provided information on the relative abundance of the RNAs, and their 5′-and 3′-termini. The study demonstrated that three highly abundant snoRNAs are involved in rRNA processing and highlight the unique trypanosome-specific repertoire of these RNAs. Novel RNAs were studied using in situ hybridization, association in RNP complexes, and 'RNA walk' to detect interaction with their target RNAs. Finally, we showed that the abundance of certain ncRNAs varies between the two stages of the parasite, suggesting that ncRNAs may contribute to gene regulation during the complex parasite's life cycle. This is the first study to provide a whole-genome analysis of the large repertoire of small RNPs in trypanosomes.

Original languageEnglish
Pages (from-to)1282-1298
Number of pages17
JournalNucleic Acids Research
Issue number3
StatePublished - Feb 2012

Bibliographical note

Funding Information:
Israel-US Binational Science Foundation (BSF); National Institutes of Health (RO1 AI056333 to E.U.); David and Inez Myers Chair in RNA silencing of diseases (to S.M.); ERC Starting Grant (to R.S.); the Minerva Foundation (to R.S.); the Azrieli Foundation (to O.W.). Funding for open access charge: National Institutes of Health (RO1 AI056333 to E.U.).


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