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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

Profile of the Solexa Sequencing DataA, length distribution of sequenced small RNAs. Small RNA reads with a length of 22 nt were the most abundant, followed by 21 and 23 nt reads. B, total sRNA annotations. C, unique sRNA annotations.
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fig23640: Profile of the Solexa Sequencing DataA, length distribution of sequenced small RNAs. Small RNA reads with a length of 22 nt were the most abundant, followed by 21 and 23 nt reads. B, total sRNA annotations. C, unique sRNA annotations.

Mentions: High-throughput sequencing was performed using small RNAs from the liver of the second filial generation tree shrew. After eliminating 3’ adapter , 5’ adapter contaminants, insert , smaller than 18 nucleotides (nts) and poly A sequences, we obtained 17503248 high-quality clean reads, accounting for 94.37% of the total raw reads, among which 14207005 reads were mapped to the Tupaia belangeri genome. Further analysis showed the majority of the small RNAs were 21 - 23 nt in size, accounting for 76.29% of the total clean reads (Figure 1A). MicroRNAs comprised 79.8% of the total small RNAs (Figure 1B), which accounted for only 12.8% of the total number of unique small RNAs (Figure 1C).


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)

Profile of the Solexa Sequencing DataA, length distribution of sequenced small RNAs. Small RNA reads with a length of 22 nt were the most abundant, followed by 21 and 23 nt reads. B, total sRNA annotations. C, unique sRNA annotations.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig23640: Profile of the Solexa Sequencing DataA, length distribution of sequenced small RNAs. Small RNA reads with a length of 22 nt were the most abundant, followed by 21 and 23 nt reads. B, total sRNA annotations. C, unique sRNA annotations.
Mentions: High-throughput sequencing was performed using small RNAs from the liver of the second filial generation tree shrew. After eliminating 3’ adapter , 5’ adapter contaminants, insert , smaller than 18 nucleotides (nts) and poly A sequences, we obtained 17503248 high-quality clean reads, accounting for 94.37% of the total raw reads, among which 14207005 reads were mapped to the Tupaia belangeri genome. Further analysis showed the majority of the small RNAs were 21 - 23 nt in size, accounting for 76.29% of the total clean reads (Figure 1A). MicroRNAs comprised 79.8% of the total small RNAs (Figure 1B), which accounted for only 12.8% of the total number of unique small RNAs (Figure 1C).

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