Differential expression profiles of miRNAs and their putative targets in Schistosoma mansoni during its life cycle

BACKGROUND Schistosomiasis is a disease caused by Schistosoma. Due to its complex life cycle, evolutionary position and sexual dimorphism, schistosomes have several mechanisms of gene regulation. MicroRNAs (miRNAs) are short endogenous RNAs that regulate gene expression at the post-transcriptional level by targeting mRNA transcripts. OBJECTIVES Here, we tested 12 miRNAs and identified their putative targets using a computational approach. METHODS We performed the expression profiles of a set of miRNAs and their putative targets during the parasite's life cycle by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). FINDINGS Our results showed differential expression patterns of the mature miRNAs sma-miR-250; sma-miR-92a; sma-miR-new_4-3p; sma-miR-new_4-5p; sma-miR-new_5-5p; sma-miR-new_12-5p; sma-miR-new_13-3p and sma-miR-new_13-5p. Interestingly, many of the putative target genes are linked to oxidative phosphorylation and are up-regulated in adult-worms, which led us to suggest that miRNAs might play important roles in the post-transcriptional regulation of genes related to energetic metabolism inversion during parasite development. It is noteworthy that the expression of sma-miR-new_13-3p exhibited a negative correlation on SmNADH:ubiquinone oxidoreductase complex I. MAIN CONCLUSIONS Our analysis revealed putative miRNA genes related to important biological processes, such as transforming growth factor beta (TGF-β) signaling, proteasome regulation, glucose and lipid metabolism, immune system evasion and transcriptional regulation.

Transcriptome-wide identification and profiling of miRNAs in a stress-tolerant conifer Sabina chinensis

miRNAs are important regulatory components involving in many biological processes, including plantdevelopment, vegetative and reproductive growth, and stress response. However, identification and characterization of miRNAs still remain limited for conifer species. In this study, with deep sequencing, we obtained1,314,450 unique reads with 18–30 nt length from a stress-tolerant conifer, Sabina chinensis. We identified 37conserved and 103 novel miRNAs, their unique characteristics were further analyzed, and 10 randomlyselected were validated by qRT-PCR. Through miRNA target predictions and annotations, we found miRNAmay have several targets as well a target could be regulated by several miRNAs, and a total of 2,397 mRNAswere predicted to be targets of the 140 miRNAs. These targets included not only important transcription factorssuch as auxin response factors, but also indispensable non-transcriptional factor proteins. Pathway-basedanalysis showed that S. chinensis miRNAs are involved in 172 metabolic pathways, of which 3 were discovered in adaptation-related pathways, indicating their possible relevance to the species’ stress-tolerancecharacteristics. This study is expected to lay the foundation for exploring the regulative roles of miRNAs indevelopment, growth, and response to environmental stresses of S. chinensis.

Computational Prediction of miR130a Target Genes in Cancer

@#Introduction: Cancer is one of the main causes of mortality globally and the incidence has been rising over the years. Studies have shown that miRNAs have the potential as cancer biomarkers. The miR-130a has been reported to be upregulated in several types of cancer, which indicate the important roles of miR-130a in cancer development and metastasis. The aim of this study is to identify potential target genes and to predict the regulatory function of miR130a-3p and 5p in cancer. Methods: Three bioinformatics platforms namely miRWalk, the Database for annotations, visualization and integrated discovery (DAVID) Gene Functional Classification Tool and miRanda-miRSVR analysis tools were used to identify possible interaction between miR-130a and its target. Protein-protein interaction (PPI) network for the predicted target genes was then constructed. Results: The analyses have identified nine predicted target genes for miR-130a-3p (RAPGEF4, SOS2, NRP1, RPS6KB1, MET, IL15, ACVR1, RYR2 and ITPR1), and ten for miR-130a-5p (BCL11A, SPOPL, NLK, PPARGC1A, POU4F2, CPEB4, ST18, RSBN1L, ELF5 and ARID4B), that might play an important role in the development of cancer. Findings from this report suggest that miR-130a may involves in controlling cancer related genes; MET, ACVR1 and BCL11A. miR-130a-3p may regulates MET which involves in apoptosis and metastasis, and ACVR1 which involves in metastasis and angiogenesis. miR-130a-5p may regulates BCL11A which involves in apoptosis, proliferation and tumorigenesis. Conclusion: This study has highlighted the molecular interaction of miR-130a with associated genes and pathways, suggesting therapeutic potential of miR130a as personalised targeted therapy for cancer.

Computational Identification of microRNAs and Their Targets / 中国生物工程杂志

The discovery of microRNAs (miRNAs) has introduced a new paradigm into gene regulatory systems. Since inception, computational methods have been an invaluable tool complementing experimental approaches, and many discoveries have been obtained through combination of experimental and computational approaches. The knowledge that has been accumulated about the principles of miRNAs and target recognition were reviewed. The currently available computational methodologies and software for prediction of miRNA and their target genes also have been discussed.

Computational Identification of microRNAs and Their Targets / 中国生物工程杂志

The discovery of microRNAs (miRNAs) has introduced a new paradigm into gene regulatory systems. Since inception, computational methods have been an invaluable tool complementing experimental approaches, and many discoveries have been obtained through combination of experimental and computational approaches. The knowledge that has been accumulated about the principles of miRNAs and target recognition were reviewed. The currently available computational methodologies and software for prediction of miRNA and their target genes also have been discussed.

Computational Identification of microRNAs and Their Targets / 中国生物工程杂志

The discovery of microRNAs (miRNAs) has introduced a new paradigm into gene regulatory systems. Since inception, computational methods have been an invaluable tool complementing experimental approaches, and many discoveries have been obtained through combination of experimental and computational approaches. The knowledge that has been accumulated about the principles of miRNAs and target recognition were reviewed. The currently available computational methodologies and software for prediction of miRNA and their target genes also have been discussed.