Discovery and characterization of medaka miRNA genes by next generation sequencing platform View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-12-02

AUTHORS

Sung-Chou Li, Wen-Ching Chan, Meng-Ru Ho, Kuo-Wang Tsai, Ling-Yueh Hu, Chun-Hung Lai, Chun-Nan Hsu, Pung-Pung Hwang, Wen-chang Lin

ABSTRACT

BACKGROUND: MicroRNAs (miRNAs) are endogenous non-protein-coding RNA genes which exist in a wide variety of organisms, including animals, plants, virus and even unicellular organisms. Medaka (Oryzias latipes) is a useful model organism among vertebrate animals. However, no medaka miRNAs have been investigated systematically. It is beneficial to conduct a genome-wide miRNA discovery study using the next generation sequencing (NGS) technology, which has emerged as a powerful sequencing tool for high-throughput analysis. RESULTS: In this study, we adopted ABI SOLiD platform to generate small RNA sequence reads from medaka tissues, followed by mapping these sequence reads back to medaka genome. The mapped genomic loci were considered as candidate miRNAs and further processed by a support vector machine (SVM) classifier. As result, we identified 599 novel medaka pre-miRNAs, many of which were found to encode more than one isomiRs. Besides, additional minor miRNAs (also called miRNA star) can be also detected with the improvement of sequencing depth. These quantifiable isomiRs and minor miRNAs enable us to further characterize medaka miRNA genes in many aspects. First of all, many medaka candidate pre-miRNAs position close to each other, forming many miRNA clusters, some of which are also conserved across other vertebrate animals. Secondly, during miRNA maturation, there is an arm selection preference of mature miRNAs within precursors. We observed the differences on arm selection preference between our candidate pre-miRNAs and their orthologous ones. We classified these differences into three categories based on the distribution of NGS reads. Finally, we also investigated the relationship between conservation status and expression level of miRNA genes. We concluded that the evolutionally conserved miRNAs were usually the most abundant ones. CONCLUSIONS: Medaka is a widely used model animal and usually involved in many biomedical studies, including the ones on development biology. Identifying and characterizing medaka miRNA genes would benefit the studies using medaka as a model organism. More... »

PAGES

s8-s8

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-11-s4-s8

DOI

http://dx.doi.org/10.1186/1471-2164-11-s4-s8

DIMENSIONS

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PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/21143817


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33 schema:description BACKGROUND: MicroRNAs (miRNAs) are endogenous non-protein-coding RNA genes which exist in a wide variety of organisms, including animals, plants, virus and even unicellular organisms. Medaka (Oryzias latipes) is a useful model organism among vertebrate animals. However, no medaka miRNAs have been investigated systematically. It is beneficial to conduct a genome-wide miRNA discovery study using the next generation sequencing (NGS) technology, which has emerged as a powerful sequencing tool for high-throughput analysis. RESULTS: In this study, we adopted ABI SOLiD platform to generate small RNA sequence reads from medaka tissues, followed by mapping these sequence reads back to medaka genome. The mapped genomic loci were considered as candidate miRNAs and further processed by a support vector machine (SVM) classifier. As result, we identified 599 novel medaka pre-miRNAs, many of which were found to encode more than one isomiRs. Besides, additional minor miRNAs (also called miRNA star) can be also detected with the improvement of sequencing depth. These quantifiable isomiRs and minor miRNAs enable us to further characterize medaka miRNA genes in many aspects. First of all, many medaka candidate pre-miRNAs position close to each other, forming many miRNA clusters, some of which are also conserved across other vertebrate animals. Secondly, during miRNA maturation, there is an arm selection preference of mature miRNAs within precursors. We observed the differences on arm selection preference between our candidate pre-miRNAs and their orthologous ones. We classified these differences into three categories based on the distribution of NGS reads. Finally, we also investigated the relationship between conservation status and expression level of miRNA genes. We concluded that the evolutionally conserved miRNAs were usually the most abundant ones. CONCLUSIONS: Medaka is a widely used model animal and usually involved in many biomedical studies, including the ones on development biology. Identifying and characterizing medaka miRNA genes would benefit the studies using medaka as a model organism.
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41 NGS
42 RNA genes
43 RNA sequences
44 abundant ones
45 additional minor miRNAs
46 analysis
47 animals
48 arm selection preference
49 aspects
50 biology
51 biomedical studies
52 candidate miRNAs
53 candidate pre-miRNAs position
54 candidates
55 categories
56 characterization
57 classifier
58 clusters
59 conservation status
60 depth
61 development biology
62 differences
63 discovery
64 discovery studies
65 distribution
66 distribution of NGS
67 expression levels
68 generation sequencing platforms
69 generation sequencing technology
70 genes
71 genome
72 genome-wide miRNA discovery study
73 genomic loci
74 high-throughput analysis
75 improvement
76 isomiRs
77 levels
78 loci
79 machine classifier
80 maturation
81 mature miRNAs
82 medaka
83 medaka candidate pre-miRNAs position
84 medaka genome
85 medaka miRNA genes
86 medaka miRNAs
87 medaka pre-miRNAs
88 medaka tissues
89 miRNA cluster
90 miRNA discovery study
91 miRNA genes
92 miRNA maturation
93 miRNAs
94 microRNAs
95 minor miRNAs
96 model animals
97 model organisms
98 next-generation sequencing platforms
99 next-generation sequencing technologies
100 novel medaka pre-miRNAs
101 one
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103 orthologous ones
104 plants
105 platform
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108 pre-miRNAs
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110 precursors
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113 relationship
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