The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi

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.

RNA干扰（RNA interference）通路广泛存在于后生动物（metazoans）中，参与从基因沉默、染色质重塑到抵御逆转录转座等诸多细胞生理过程。单细胞真核生物克氏锥虫（Trypanosoma cruzi）缺失经典RNA干扰通路，无法诱发RNA干扰相关的生物学过程。为深入解析该生物体内的替代性RNA通路，我们针对其上鞭毛体（epimastigote）生活史阶段的大小分级cDNA文库（16–61 nt）开展了深度测序与全基因组分析。本次深度测序共获得582243条短序列，其中91%可比对至该物种的基因组序列。约95%至98%的比对数据（因单倍型（haplotype）不同而存在差异）对应于源自转运RNA（transfer RNAs, tRNAs）、核糖体RNA（ribosomal RNAs, rRNAs）、小核RNA（small nuclear RNAs, snRNAs）与小核仁RNA（small nucleolar RNAs, snoRNAs）的小RNA（small RNAs）。占比最高的类别为tRNA来源的小RNA，其主要起源于tRNA的3′端，其次为rRNA来源的小RNA。剩余序列则揭示了92个全新的转录基因座，其中79个未与已知RNA类别存在同源性。