Limits...
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

Characteristics of the Conserved MicroRNA and the MiR-122 Family in Tree ShrewA, expression of miRNAs of which the expression level occupied the top 20 of all conserved miRNAs. B, the pie chart of the percentage of miR-122 and Let-7 in the tree shrew liver miRNAs. C, expression of four members of miR-122 family in tree shrew. D, the secondary structures of the four precursors of miR-122 in human, tree shrew, mice and rat.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4644573&req=5

fig23641: Characteristics of the Conserved MicroRNA and the MiR-122 Family in Tree ShrewA, expression of miRNAs of which the expression level occupied the top 20 of all conserved miRNAs. B, the pie chart of the percentage of miR-122 and Let-7 in the tree shrew liver miRNAs. C, expression of four members of miR-122 family in tree shrew. D, the secondary structures of the four precursors of miR-122 in human, tree shrew, mice and rat.

Mentions: To identify conserved miRNAs in our data, the sorted clean sRNA reads were aligned with the mature miRNAs in miRBase 20.0 (http://www.mirbase.org/). As a result, 2060 unique small RNAs were identified to be matched with the known miRNAs. Expression levels of miRNAs that occupied the top 20 of all identified miRNAs are shown in Figure 2A. The most abundant conserved miRNA identified in the library was miR-122, with more than 9000000 reads, which accounted for 69.1% of the total miRNAs (Figure 2B). Four types of unique small RNA, belonging to the miR-122 family, were identified and nominated as tsh-miR-122, tsh-miR-122-5p, tsh-miR-122b and tsh-miR-122-3p, respectively. Expression levels of these four miRNAs were shown in Figure 2C. The abundance of tsh-miR-122 and tsh-miR-122-5p was much higher than that of tsh-miR-122b and tsh-miR-122-3p. The precursor of tsh-miR-122 was subjected to further analysis, by comparing with miR-122 precursors of 18 animal species, derived from the miRBase. It was shown that the sequence of the precursor of miR-122 of tree shrew was most identical with that of human (Figure 3). In addition, the secondary structure and the energy of primary miRNA of tree shrew for miR-122 were also similar with that of human (Figure 2D).


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)

Characteristics of the Conserved MicroRNA and the MiR-122 Family in Tree ShrewA, expression of miRNAs of which the expression level occupied the top 20 of all conserved miRNAs. B, the pie chart of the percentage of miR-122 and Let-7 in the tree shrew liver miRNAs. C, expression of four members of miR-122 family in tree shrew. D, the secondary structures of the four precursors of miR-122 in human, tree shrew, mice and rat.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig23641: Characteristics of the Conserved MicroRNA and the MiR-122 Family in Tree ShrewA, expression of miRNAs of which the expression level occupied the top 20 of all conserved miRNAs. B, the pie chart of the percentage of miR-122 and Let-7 in the tree shrew liver miRNAs. C, expression of four members of miR-122 family in tree shrew. D, the secondary structures of the four precursors of miR-122 in human, tree shrew, mice and rat.
Mentions: To identify conserved miRNAs in our data, the sorted clean sRNA reads were aligned with the mature miRNAs in miRBase 20.0 (http://www.mirbase.org/). As a result, 2060 unique small RNAs were identified to be matched with the known miRNAs. Expression levels of miRNAs that occupied the top 20 of all identified miRNAs are shown in Figure 2A. The most abundant conserved miRNA identified in the library was miR-122, with more than 9000000 reads, which accounted for 69.1% of the total miRNAs (Figure 2B). Four types of unique small RNA, belonging to the miR-122 family, were identified and nominated as tsh-miR-122, tsh-miR-122-5p, tsh-miR-122b and tsh-miR-122-3p, respectively. Expression levels of these four miRNAs were shown in Figure 2C. The abundance of tsh-miR-122 and tsh-miR-122-5p was much higher than that of tsh-miR-122b and tsh-miR-122-3p. The precursor of tsh-miR-122 was subjected to further analysis, by comparing with miR-122 precursors of 18 animal species, derived from the miRBase. It was shown that the sequence of the precursor of miR-122 of tree shrew was most identical with that of human (Figure 3). In addition, the secondary structure and the energy of primary miRNA of tree shrew for miR-122 were also similar with that of human (Figure 2D).

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