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Identification and Characterization of Liver MicroRNAs of the Chinese Tree Shrew via Deep Sequencing.

Feng Y, Feng YM, Feng Y, Lu C, Liu L, Sun X, Dai J, Xia X - Hepat Mon (2015)

Bottom Line: Moreover, 80 novel microRNAs were predicted using the software Mireap.The top 3 abundant miRNAs were validated in other tree samples, based on stem-loop quantitative reverse transcription-polymerase chain reaction.According to the liver microRNA data of Chinese tree shrew, characteristics of the miR-122 and Let-7 families further highlight the suitability of tree shrew as the animal model in HCV research.

View Article: PubMed Central - PubMed

Affiliation: Yunnan Provincial Center for Molecular Medicine, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.

ABSTRACT

Background: Chinese tree shrew (Tupaia belangeri chinensis) is a small animal that possess many features, which are valuable in biomedical research, as experimental models. Currently, there are numerous attempts to utilize tree shrews as models for hepatitis C virus (HCV) infection.

Objectives: This study aimed to construct a liver microRNA (miRNA) data of the tree shrew.

Materials and methods: Three second filial generation tree shrews were used in this study. Total RNA was extracted from each liver of the tree shrew and equal quality mixed, then reverse-transcribed to complementary DNA (cDNA). The cDNAs were amplified by polymerase chain reaction and subjected to high-throughput sequencing.

Results: A total of 2060 conserved miRNAs were identified through alignment with the mature miRNAs in miRBase 20.0 database. The gene ontology and Kyoto encyclopedia of genes and genomes analyses of the target genes of the miRNAs revealed several candidate miRNAs, genes and pathways that may involve in the process of HCV infection. The abundance of miR-122 and Let-7 families and their other characteristics provided us more evidences for the utilization of this animal, as a potential model for HCV infection and other related biomedical research. Moreover, 80 novel microRNAs were predicted using the software Mireap. The top 3 abundant miRNAs were validated in other tree samples, based on stem-loop quantitative reverse transcription-polymerase chain reaction.

Conclusions: According to the liver microRNA data of Chinese tree shrew, characteristics of the miR-122 and Let-7 families further highlight the suitability of tree shrew as the animal model in HCV research.

No MeSH data available.


Related in: MedlinePlus

The Gene Ontology Enrichment Analysis of Predicted Targets of Differentially Expressed MicroRNAs With P < 0.05A total of 36007 putative target genes were assigned to the GO annotations of Biological Process (11519), Cellular Component (12110), and Molecular Function (12378). The GO terms were sorted by the enrichment P value calculated by the calculating formula as previously described (8). A, biological process, B, molecular function, C, cellular component.
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fig23645: The Gene Ontology Enrichment Analysis of Predicted Targets of Differentially Expressed MicroRNAs With P < 0.05A total of 36007 putative target genes were assigned to the GO annotations of Biological Process (11519), Cellular Component (12110), and Molecular Function (12378). The GO terms were sorted by the enrichment P value calculated by the calculating formula as previously described (8). A, biological process, B, molecular function, C, cellular component.

Mentions: To identify the functions and pathways that the miRNAs and their targets may affect, GO and KEGG pathway analyses were performed. GO analysis showed that 32% of the genes were annotated to biological processes, 34.4% of the genes mapped to molecular function and 33.6% of the genes were composed of cellular component. These genes ranged from elevation of cytosolic calcium ion concentration to regulation of signaling pathway, genes regulating sodium channel activity to genes regulating phosphatase binding and genes regulating microvillus to genes regulating plasma membrane (Figure 6). The findings revealed that predicted targets of miRNAs were associated with a wide variety of biological processes. Furthermore, for KEGG pathway analysis, some classic pathways reported to involve in immunoregulation were found in this study, including Toll-like receptor signaling pathway, B cell receptor signaling pathway, T cell receptor signaling pathway, Natural killer cell mediated cytotoxicity and so on (Figure 7). Intriguingly, Hepatitis C was also enriched from the predicted targets, suggesting that these targets play important roles in the process of infection and inflammation. Taken together, GO and KEGG analyses supply a better understanding of the cellular components, molecular functions and biological processes of target genes, and provided a reference for future study.


Identification and Characterization of Liver MicroRNAs of the Chinese Tree Shrew via Deep Sequencing.

Feng Y, Feng YM, Feng Y, Lu C, Liu L, Sun X, Dai J, Xia X - Hepat Mon (2015)

The Gene Ontology Enrichment Analysis of Predicted Targets of Differentially Expressed MicroRNAs With P < 0.05A total of 36007 putative target genes were assigned to the GO annotations of Biological Process (11519), Cellular Component (12110), and Molecular Function (12378). The GO terms were sorted by the enrichment P value calculated by the calculating formula as previously described (8). A, biological process, B, molecular function, C, cellular component.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4644573&req=5

fig23645: The Gene Ontology Enrichment Analysis of Predicted Targets of Differentially Expressed MicroRNAs With P < 0.05A total of 36007 putative target genes were assigned to the GO annotations of Biological Process (11519), Cellular Component (12110), and Molecular Function (12378). The GO terms were sorted by the enrichment P value calculated by the calculating formula as previously described (8). A, biological process, B, molecular function, C, cellular component.
Mentions: To identify the functions and pathways that the miRNAs and their targets may affect, GO and KEGG pathway analyses were performed. GO analysis showed that 32% of the genes were annotated to biological processes, 34.4% of the genes mapped to molecular function and 33.6% of the genes were composed of cellular component. These genes ranged from elevation of cytosolic calcium ion concentration to regulation of signaling pathway, genes regulating sodium channel activity to genes regulating phosphatase binding and genes regulating microvillus to genes regulating plasma membrane (Figure 6). The findings revealed that predicted targets of miRNAs were associated with a wide variety of biological processes. Furthermore, for KEGG pathway analysis, some classic pathways reported to involve in immunoregulation were found in this study, including Toll-like receptor signaling pathway, B cell receptor signaling pathway, T cell receptor signaling pathway, Natural killer cell mediated cytotoxicity and so on (Figure 7). Intriguingly, Hepatitis C was also enriched from the predicted targets, suggesting that these targets play important roles in the process of infection and inflammation. Taken together, GO and KEGG analyses supply a better understanding of the cellular components, molecular functions and biological processes of target genes, and provided a reference for future study.

Bottom Line: Moreover, 80 novel microRNAs were predicted using the software Mireap.The top 3 abundant miRNAs were validated in other tree samples, based on stem-loop quantitative reverse transcription-polymerase chain reaction.According to the liver microRNA data of Chinese tree shrew, characteristics of the miR-122 and Let-7 families further highlight the suitability of tree shrew as the animal model in HCV research.

View Article: PubMed Central - PubMed

Affiliation: Yunnan Provincial Center for Molecular Medicine, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.

ABSTRACT

Background: Chinese tree shrew (Tupaia belangeri chinensis) is a small animal that possess many features, which are valuable in biomedical research, as experimental models. Currently, there are numerous attempts to utilize tree shrews as models for hepatitis C virus (HCV) infection.

Objectives: This study aimed to construct a liver microRNA (miRNA) data of the tree shrew.

Materials and methods: Three second filial generation tree shrews were used in this study. Total RNA was extracted from each liver of the tree shrew and equal quality mixed, then reverse-transcribed to complementary DNA (cDNA). The cDNAs were amplified by polymerase chain reaction and subjected to high-throughput sequencing.

Results: A total of 2060 conserved miRNAs were identified through alignment with the mature miRNAs in miRBase 20.0 database. The gene ontology and Kyoto encyclopedia of genes and genomes analyses of the target genes of the miRNAs revealed several candidate miRNAs, genes and pathways that may involve in the process of HCV infection. The abundance of miR-122 and Let-7 families and their other characteristics provided us more evidences for the utilization of this animal, as a potential model for HCV infection and other related biomedical research. Moreover, 80 novel microRNAs were predicted using the software Mireap. The top 3 abundant miRNAs were validated in other tree samples, based on stem-loop quantitative reverse transcription-polymerase chain reaction.

Conclusions: According to the liver microRNA data of Chinese tree shrew, characteristics of the miR-122 and Let-7 families further highlight the suitability of tree shrew as the animal model in HCV research.

No MeSH data available.


Related in: MedlinePlus