The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi

• Published in: PLoS neglected tropical diseases Vol. 5; no. 8; p. e1283
• Main Authors: Franzén, Oscar, Arner, Erik, Ferella, Marcela, Nilsson, Daniel, Respuela, Patricia, Carninci, Piero, Hayashizaki, Yoshihide, Aslund, Lena, Andersson, Björn, Daub, Carsten O
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.08.2011; Public Library of Science (PLoS)
• Subjects: Biology; Chagas' disease; Gene Library; Genetic aspects; Genetics; Genomes; Haplotypes; High-Throughput Nucleotide Sequencing; Medicin och hälsovetenskap; Parasites; Protozoa; Ribonucleic acid; Risk factors; RNA; RNA polymerase; RNA, Untranslated - genetics; Sequence Analysis, DNA; Transcriptome; Tropical diseases; Trypanosoma cruzi; Trypanosoma cruzi - genetics; Switzerland; Sweden; Japan; Latin America; High-Throughput Nucleotide Sequencing; Gene Library; Sequence Analysis, DNA; RNA, Untranslated; Transcriptome; Trypanosoma cruzi
• ISSN: 1935-2735; 1935-2727; 1935-2735
• DOI: 10.1371/journal.pntd.0001283

The pathway for RNA interference is widespread in metazoans and participates in numerous cellular tasks, from gene silencing to chromatin remodeling and protection against retrotransposition. The unicellular eukaryote Trypanosoma cruzi is missing the canonical RNAi pathway and is unable to induce RNAi-related processes. To further understand alternative RNA pathways operating in this organism, we have performed deep sequencing and genome-wide analyses of a size-fractioned cDNA library (16-61 nt) from the epimastigote life stage. Deep sequencing generated 582,243 short sequences of which 91% could be aligned with the genome sequence. About 95-98% of the aligned data (depending on the haplotype) corresponded to small RNAs derived from tRNAs, rRNAs, snRNAs and snoRNAs. The largest class consisted of tRNA-derived small RNAs which primarily originated from the 3' end of tRNAs, followed by small RNAs derived from rRNA. The remaining sequences revealed the presence of 92 novel transcribed loci, of which 79 did not show homology to known RNA classes.