Transcriptomics

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MiRNA expression profile analysis of Clonorchis sinensis by Solexa deep sequencing


ABSTRACT: Clonorchis sinensis is a zoonotic parasite causing clonorchiasis associated with human diseases such as biliary calculi, cholecystitis, liver cirrhosis, and is classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules essential for the complex life cycle of parasites and 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, bioinformatic predictions with stem-loop real-time PCR analysis. Here we report the use of this approach to identify and clone 6 new and 62,512 conserved C. sinensis miRNAs which belong to 284 families. There is strong bias on families, family members and sequence nucleotides in C. sinensis. Uracil is the dominant nucleotide, particularly at positions 1, 14 and 22, which were located approximately at the beginning, middle and the end of conserved miRNAs. There is no significant “seed region” at the first and ninth positions commonly found in human, animals and plants. Categorization of conserved miRNAs indicated that miRNAs of C. sinensis are still innovated and concentrated along three branches of the phylogenetic tree leading to bilaterians, insects and coelomates. There are two miRNA strategies in C. sinensis for its parasitic life: keeping a large category of miRNA families of different animals and keeping a stringent conserved seed region with high active innovation in other place of miRNA mainly in the middle and the end, which are perfect for the parasite to perform its complex life style and for host changes. The present study represents the first large scale characterization of C. sinensis miRNAs, which have implications for understanding the complex biology of this zoonotic parasite, as well as the miRNA studies of other related species such as Opisthorchis felineus and O. viverrini of human and animal health significance. Analysis of miRNA profile in parasite of C. sinensis

ORGANISM(S): Clonorchis sinensis  

SUBMITTER: Zhu Xingquan   Xu Minjun 

PROVIDER: E-GEOD-22244 | ArrayExpress | 2010-09-03

SECONDARY ACCESSION(S): SRP002596GSE22244PRJNA127731

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Identification and characterization of microRNAs in Clonorchis sinensis of human health significance.

Xu Min-Jun MJ   Liu Quan Q   Nisbet Alasdair J AJ   Cai Xian-Quan XQ   Yan Chao C   Lin Rui-Qing RQ   Yuan Zi-Guo ZG   Song Hui-Qun HQ   He Xian-Hui XH   Zhu Xing-Quan XQ  

BMC genomics 20100928


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  ...[more]

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