Expression Profiles Analysis And Target Prediction Of Sexual Micrornas From Strongylocentrotus Nudus Gonad

MicroRNAs （miRNAs） are a class of endogenous small non-coding RNAs that regulategene expression by post-transcriptional repression of messenger RNA. This kind ofnon-coding RNAs play important roles in the biological process of animal such as individualdevelopment, cell differentiation and organogenesis. The echinoderms, Sea urchin, is anexcellent model organism for studying development and commercially important as a foodsource for its gonad. However, to date no miRNAs have been reported to modulate sex gonaddifferentiation in sea urchin. In this study, we constructed two small RNA libraries from maleand female S. nudus gonad respectively for Solexa sequencing. A number of known and novelmiRNAs were identified and differently expressed anlysis was performed between the twolibraries. Besides, we performed target prediction of the differented expressed miRNAs andGO functional annotation of the targets. This study reveals the first miRNA profile related tothe gonad differentiation of the S. nudus. This study gives a first insight into sex differences inmiRNA expression of sea urchin which could facilitate studies of the reproductiveorgan-specific roles of miRNAsThe main conclusions are:1. According to the sequenced results of the three admixed female gonad samples andthree admixed male gonad samples of sea urchin, there are7,012,368reads of raw data and2,146,398reads of clean data from the male gonad tissue, and15,159,991reads of raw dataand8,522,275reads of clean data from the female gonad2. After mapped to miRNA database and sea urchin genome, a total of66conservativemiRNAs were identified. According to the criterias of pre-miRNAs secondary stem structure,a total of118novel miRNAs were predicted in this study.3. Different analysis of miRNAs between the two samples shows that in the total of184miRNAs,47miRNAs （25.54%） were male-specific,51miRNAs （27.72%） female-specificand the other86miRNAs （46.74%） were co-expressed. Among the co-expressed miRNAs,39were down-regulated and28were higher in female gonad significantly.4. Real-time quantitative PCR technology was performed for four significantlydifferently expressed miRNAs （spu-miR-71, spu-miR-31, PC-3p-80₂7784andPC-3p-3587₁221）, which is consistent with the expression profile via sequencing. 5. Targetscan and miRanda software were combined to predict target genes of top10up-regualated miRNAs and top10down-regulated miRNAs in female gonad tissue comparedto male gonad. As a result,6699and4666targets were predicted respectively.6. GO function annotation was performed for the targets of the two groups of top tendifferently expressed miRNA. They have similar gene function and may be associated withgonad tissue differentiation and fatty acid metabolism.In conclusion, we have identified66conserved miRNAs and118novel miRNAs ingonad tissue from male and female S. nudus using Solexa deep sequencing technologies. ThemiRNA expression patterns from male and female S. nudus showed that most miRNAs aredifferently expressed in different gender samples, suggesting that these miRNAs may play arole in gonad differentiation biological processes.Sea urchin was the ideal model of theevolutionary biology and developmental biology study, and miRNA played an important rolein evolutionary development as an important class of gene regulatory factors. Screening andfunction studying of miRNA in sea urchin provides groundwork for further research ofmolecular mechanism of gonad development and sex differentiation of sea urchin. What’smore, it will contribute to a better understanding of the molecular mechanism of sexdetermination, reproductive development and pathologies in animals, which finally benefitshumans.