title: RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs.
abstract: 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.
authors: The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel. michaes@mail.biu.ac.il
authors: Shulamit
authors: S
authors: Michaeli
authors: Tirza
authors: T
authors: Doniger
authors: Sachin Kumar
authors: SK
authors: Gupta
authors: Omri
authors: O
authors: Wurtzel
authors: Mali
authors: M
authors: Romano
authors: Damian
authors: D
authors: Visnovezky
authors: Rotem
authors: R
authors: Sorek
authors: Ron
authors: R
authors: Unger
authors: Elisabetta
authors: E
authors: Ullu
mesh_terms: D002478:Cells, Cultured; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D009690:Nucleic Acid Conformation; D012323:RNA Processing, Post-Transcriptional; D016053:RNA, Protozoan / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D012335:RNA, Ribosomal / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D012261:Ribonucleoproteins / Q000302:isolation & purification; D017423:Sequence Analysis, RNA; D014346:Trypanosoma brucei brucei / Q000235:genetics*
chemical_list: D016053:RNA, Protozoan; D012335:RNA, Ribosomal; D020537:RNA, Small Nucleolar; D058727:RNA, Small Untranslated; D012261:Ribonucleoproteins