An “In-Depth” Description of the Small Non-coding RNA Population of Schistosoma japonicum Schistosomulum

Abstract

Parasitic flatworms of the genus Schistosoma are the causative agents of schistosomiasis, which afflicts more than 200 million people yearly in tropical regions of South America, Asia and Africa. A promising approach to the control of this and many other diseases involves the application of our understanding of small non-coding RNA function to the design of safe and effective means of treatment. In a previous study, we identified five conserved miRNAs from the adult stage of Schistosoma japonicum. Here, we applied Illumina Solexa high-throughput sequencing methods (deep sequencing) to investigate the small RNAs expressed in S. japonicum schistosomulum (3 weeks post-infection). This has allowed us to examine over four million sequence reads including both frequently and infrequently represented members of the RNA population. Thus we have identified 20 conserved miRNA families that have orthologs in well-studied model organisms and 16 miRNA that appear to be specific to Schistosoma. We have also observed minor amounts of heterogeneity in both 3′ and 5′ terminal positions of some miRNA as well as RNA fragments resulting from the processing of miRNA precursor. An investigation of the genomic arrangement of the 36 identified miRNA revealed that seven were tightly linked in two clusters. We also identified members of the small RNA population whose structure indicates that they are part of an endogenously derived RNA silencing pathway, as evidenced by their extensive complementarities with retrotransposon and retrovirus-related Pol polyprotein from transposon.

Comparative analysis of known miRNAs across platyhelminths

“…In flatworms, miR-61 has been reported in S. mediterranea [14] and Sc. japonicum [26]. We also found that E. multilocularis and E. granulosus harbored one miR-61 gene locus and the pre-miRNAs of miR-61 had canonical secondary structures ( Fig.…”

“…However, we did not determine the genomic locus for miR-8 using corresponding pre-miRNA sequences in platyhelminths (data not shown), expression of which has been confirmed experimentally in S. mediterranea, Sc. japonicum, E. multilocularis and E. granulosus [14,17,26]. This is explained by the heterogeneity of the miR-8 gene.…”

Advances in the Diagnosis of Human Schistosomiasis

“…Identification and characterization of a set of parasite-derived miRNAs in both S. mansoni (239,240) and S. japonicum (241)(242)(243)(244) provided the basis for their detection in the circulation. The presence of schistosome-specific miRNAs was first reported for the plasmas of S. japonicum-infected rabbits, by Cheng et al (245) and then by Hoy et al (246), who demonstrated elevations of several parasite-derived S. mansoni miRNAs, including sma-miR-277, sma-miR-3479-3p, and bantam, in a mouse model at 8 weeks postinfection.…”

Molecular cloning and expression profiles of Argonaute proteins in Schistosoma japonicum

“…In S. japonicum, it had been well established for a while that the usages of siRNAs were able to artificially induce specific endogenous mRNA degradation at transcript level (Cheng et al 2005b;Cheng et al 2009). Very recently, a considerable number of miRNAs have also been identified in different development stages of schistosomes and further studies indicated that the expression profiles of these miRNAs were associated with parasite development, suggesting that miRNAs could be involved in regulating schistosome development Hao et al 2010;Wang et al 2010). …”

“…Schistosomes have a complex life cycle associated with dramatic morphological transformations and rapid physiological adaptations, suggesting that miRNAs/siRNAs could play crucial roles in schistosome development (Cheng et al 2005b;Cheng et al 2009;Huang et al 2009;Hao et al 2010;Wang et al 2010). However, it still remains unknown how many Argonaute proteins are present in S. japonicum and whether their expression profiles are associated with parasite development.…”