Identification and characterization of microRNAs in Clonorchis sinensis of human health significance - PubMed (original) (raw)
Identification and characterization of microRNAs in Clonorchis sinensis of human health significance
Min-Jun Xu et al. BMC Genomics. 2010.
Abstract
Background: Clonorchis sinensis is a zoonotic parasite causing clonorchiasis-associated human disease such as biliary calculi, cholecystitis, liver cirrhosis, and it is currently classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules which are essential for the complex life cycles of parasites and are involved in parasitic infections. To identify and characterize miRNAs expressed in adult C. sinensis residing chronically in the biliary tract, we developed an integrative approach combining deep sequencing and bioinformatic predictions with stem-loop real-time PCR analysis.
Results: Here we report the use of this approach to identify and clone 6 new and 62,512 conserved C. sinensis miRNAs which belonged to 284 families. There was strong bias on families, family members and sequence nucleotides in C. sinensis. Uracil was the dominant nucleotide, particularly at positions 1, 14 and 22, which were located approximately at the beginning, middle and end of conserved miRNAs. There was no significant "seed region" at the first and ninth positions which were commonly found in human, animals and plants. Categorization of conserved miRNAs indicated that miRNAs of C. sinensis were still innovated and concentrated along three branches of the phylogenetic tree leading to bilaterians, insects and coelomates. There were two miRNA strategies in C. sinensis for its parasitic life: keeping a large category of miRNA families of different animals and keeping stringent conserved seed regions with high active innovation in other places of miRNAs mainly in the middle and the end, which were perfect for the parasite to perform its complex life style and for host changes.
Conclusions: The present study represented the first large scale characterization of C. sinensis miRNAs, which have implications for understanding the complex biology of this zoonotic parasite, as well as miRNA studies of other related species such as Opisthorchis viverrini and Opisthorchis felineus of human and animal health significance.
Figures
Figure 1
Length distribution of small RNAs from Clonorchis sinensis identified and analyzed by deep sequencing. Analysis of 12,138,350 high quality reads after filtering low quality tags, 5' and 3' adaptor and contamination formed by adaptor-adaptor ligation.
Figure 2
The predicted stem-loop structures for the six novel miRNA precursors in Clonorchis sinensis. The mature miRNA sequences are shown in red and underlined. The actual size of each putative precursor was not identified experimentally and may be slightly shorter or longer than represented. There are two possible stem-loop structures for cis-miR-006 and three predicted stem-loop structures for cis-miR-019, the structures of these two precursors shown in this figure are the ones recommended by the software of Mfold.
Figure 3
Phylogenetic evolution of 50 conserved miRNA families in Clonorchis sinensis. (a) Phylogenetic distribution of 50 conserved miRNA families of C. sinensis. A plus (+) symbol indicates this miRNA family exists in the species named on the left. (b and c) Phylogenetic analysis of miR-2 family shows middle evolution approach of miRNA in C. sinensis. (d and e) Phylogenetic analysis of miR-87 family shows another evolution approach of miRNA in C. sinensis which is conserved in middle and changed in the tail.
Figure 4
Analysis of first nucleotide bias of miRNAs in Clonorchis sinensis.
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