Discovery and characterization of medaka miRNA genes by next generation sequencing platform - PubMed (original) (raw)

Comparative Study

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

Sung-Chou Li et al. BMC Genomics. 2010.

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.

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Figures

Figure 1

Presentation of candidate information. Each isomiR was generated from independent sequence read and aligned as positive. Copy number denotes the abundance of each isomiR from initial read collection and represents the expression level of each isomiR. p-value denotes the probability at which one candidate was classified as a positive hit by mistake based on the SVM classification model. The term in parenthesis denotes the family to which the orthologous known pre-miRNA belongs.

Figure 2

Comparison of arm selection preference of miRNAs within precursor. Dark blue balls and light blue balls denote the location of major form and minor form of mature miRNA, respectively. Double-headed arrows demonstrate sequence conservation between candidate pre-miRNAs and their orthologous ones.

Figure 3

Box plot of expression levels of different sets ordered by conservation level. The plot illustrates that the sets are different from each other in terms of expression level. P-value denotes the result from pair-wised t-test.

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Discovery and characterization of medaka miRNA genes by next generation sequencing platform - PubMed (original) (raw)