Abstract
BackgroundHuman schistosomiasis is one of the most prevalent and serious parasitic diseases worldwide. Schistosoma japonicum is one of important pathogens of this disease. MicroRNAs (miRNAs) are a large group of non-coding RNAs that play important roles in regulating gene expression and protein translation in animals. Genome-wide identification of miRNAs in a given organism is a critical step to facilitating our understanding of genome organization, genome biology, evolution, and posttranscriptional regulation.Methodology/Principal FindingsWe sequenced two small RNA libraries prepared from different stages of the life cycle of S. japonicum, immature schistosomula and mature pairing adults, through a deep DNA sequencing approach, which yielded ∼12 million high-quality short sequence reads containing a total of ∼2 million non-redundant tags. Based on a bioinformatics pipeline, we identified 176 new S. japonicum miRNAs, of which some exhibited a differential pattern of expression between the two stages. Although 21 S. japonicum miRNAs are orthologs of known miRNAs within the metazoans, some nucleotides at many positions of Schistosoma miRNAs, such as miR-8, let-7, miR-10, miR-31, miR-92, miR-124, and miR-125, are indeed significantly distinct from other bilaterian orthologs. In addition, both miR-71 and some miR-2 family members in tandem are found to be clustered in a reversal direction model on two genomic loci, and two pairs of novel S. japonicum miRNAs were derived from sense and antisense DNA strands at the same genomic loci.Conclusions/SignificanceThe collection of S. japonicum miRNAs could be used as a new platform to study the genomic structure, gene regulation and networks, evolutionary processes, development, and host-parasite interactions. Some S. japonicum miRNAs and their clusters could represent the ancestral forms of the conserved orthologues and a model for the genesis of novel miRNAs.
Highlights
Schistosomes are members of the phylum Platyhelminthes
This result supported the hypothesis that S. japonicum is capable of generating endogenous miRNAs that carry out post-transcriptional regulation
To survey S. japonicum microRNAs and further understand their biological function, we constructed complementary DNA libraries derived from 18–30 nt RNAs isolated from both schistosomula (SC), the immature unpaired worms, and mature pairing adults (AW), respectively (Figure 1), where the pairing of schistosomes are essential for their maturation and egg-laying
Summary
Schistosomes are members of the phylum Platyhelminthes. unlike most other platyhelminths, dioecious schistosomes can cause severe human schistosomiasis, which remains one of the most prevalent and serious parasitic diseases worldwide [1]. RNA interference (RNAi) has previously been described in Schistosoma mansoni and S. japonicum, for which the addition of exogenous dsRNA resulted in a measurable suppression of target gene expression [9,10,11,12] This suggests that schistosomes possess the molecular machinery that contains an effector nuclease complex, known as the RNAinduced silencing complex (RISC), which recognizes and destroys homologous target mRNAs in an endonucleolytic manner [13,14]. A Dicer-1 like (EF204544) multi-domain nuclease that is responsible for cutting double-strand RNAs into short interfering RNAs (siRNAs) approximately 21 nucleotides (nt) long, and argonaute (Ago) effector proteins that target mRNA molecules for silencing or destruction under guidance by miRNAs, were identified in S. mansoni [15,16] This implies that miRNAs could be generated by action of Dicer and play important roles in posttranscriptional regulation. Genome-wide identification of miRNAs in a given organism is a critical step to facilitating our understanding of genome organization, genome biology, evolution, and posttranscriptional regulation
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