title: Profiles of small non-coding RNAs in Schistosoma japonicum during development.
abstract: BACKGROUND
  The gene regulation mechanism along the life cycle of the genus Schistosoma is complex. Small non-coding RNAs (sncRNAs) are essential post transcriptional gene regulation elements that affect gene expression and mRNA stability. Preliminary studies indicated that sncRNAs in schistosomal parasites are generated through different pathways, which are developmentally regulated. However, the data of sncRNAs of schistosomal parasites are still fragmental and a complete expression profile of sncRNAs during the parasite development requires a deep investigation.
  
  
  RESULTS
  We employed high-throughput genome-wide transcriptome analytic techniques to explore the dynamic expression of microRNAs (miRNAs) and endogenous siRNAs (endo-siRNAs) of Schistosoma japonicum covering the free-living cercarial stage and all stages in the definitive host. This led us to analyze over 70 million clean reads represented both high and low abundance of the small RNA population. Patterns of differential expression of miRNAs and endo-siRNAs were observed. MiRNAs was twice more than endo-siRNAs in cercariae, but gradually decreased along with the development of the parasite. Both small RNA types were presented in equal aboudance in lung-stage schistosomula, while endo-siRNAs accumulated to 6 times more than miRNAs in adult female worms and hepatic eggs. Further, miRNAs were found mainly derived from genes located in the intergenic regions, while endo-siRNAs were mainly generated from transposable elements (TEs). The expression pattern of TE-siRNAs, as well as the pseudogene-derived siRNAs clustered in mRNAs of cytoskeletal proteins, stress proteins, enzymes related to energy metabolism also revealed distinction throughout different developmental stages. Natural antisense transcripts (NATs)-related siRNAs accounted for minor proportion of the endo-siRNAs which were dominantly expressed in cercariae.
  
  
  CONCLUSIONS
  Our results represented a comprehensive expression profile of sncRNAs in various developmental stages of S. japonicum with high accuracy and coverage. The data would facilitate a deep understanding of the parasite biology and potential discovery of novel targets for the design of anti-parasite drugs.
authors.affiliation: Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Cai
authors.forename: Nan
authors.initials: N
authors.lastname: Hou
authors.forename: Xianyu
authors.initials: X
authors.lastname: Piao
authors.forename: Shuai
authors.initials: S
authors.lastname: Liu
authors.forename: Haiying
authors.initials: H
authors.lastname: Liu
authors.forename: Fan
authors.initials: F
authors.lastname: Yang
authors.forename: Jianwei
authors.initials: J
authors.lastname: Wang
authors.forename: Qi
authors.initials: Q
authors.lastname: Jin
authors.forename: Heng
authors.initials: H
authors.lastname: Wang
authors.forename: Qijun
authors.initials: Q
authors.lastname: Chen
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D004251:DNA Transposable Elements; D005260:Female; D018507:Gene Expression Regulation, Developmental; D007814:Larva; D008297:Male; D051379:Mice; D008807:Mice, Inbred BALB C; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008974:Mollusca; D034741:RNA, Small Interfering / Q000235:genetics* / Q000378:metabolism; D011817:Rabbits; D012549:Schistosoma japonicum / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D012554:Schistosomiasis japonica / Q000469:parasitology; D059467:Transcriptome
chemical_list: D004251:DNA Transposable Elements; D035683:MicroRNAs; D034741:RNA, Small Interfering