Sea Urchin microRNAome Uncovered via RNA-Seq and Microarray

Sea urchins in the genus Strongylocentrotus are important research models in many areas of bioscience including developmental and cell biology, reproductive biology and evolutionary biology. The purple urchin, specifically S.nudus is one of the most economically important marine animals as the gonads of S. nudus are extensively eaten as a delicacy in China, Korea and Japan. In China, however, natural stocks of S. nudus have declined dramatically due to overfishing and damage of natural habitat. The economic and biomedical importance of the urchin has lead to significant efforts to decode the urchin genome and its genetics. However, only 45 microRNAs are currently listed in miRBase version 16.0, laging behind other deuterostomia species.

Recently, a collaboration of researchers from a group of Life Science universities in China set out to understand the miRNA-based regulatory system of this urchin species as well as basel deuterostomia lineages. First, high throughput sequencing analysis of miRNAs was performed on a small RNA library isolated from five tissues of S. nudus. with the Illumina sequencing platform. Quality reads were filtered for miRNA prediction with the ACGT101-miR-v3.5 package. Reads that matched to rRNA, tRNA, snRNA, snoRNA, repeat sequences, and other ncRNAs deposited in Rfam 8.0, as well as to the sequences containing polyA tails, were discarded. The retained 18-26 nt reads were mapped onto the Strongylocentrotus purpuratus genome and to all deuterostoma known mature miRNA sequences in miRBase Version 16.0. The bioinformatics analysis yielded 415 unique microRNAs including 345 deuterostoma conserved and 70 urchin specific microRNAs, as well as 5 microRNA* sequences.

Next, a miRNA microarray assay was used to confirm the expression of miRNAs in female urchin gonad. A custom microarray consisting of 460 probes for miRNAs corresponding to 415 identified in this research and 45 known urchin miRNAs were designed and in situ synthesized using the µParaflo platform. One hundred miRNAs were confirmed to express at different signal values, 68 of which were identified first time in this research and others were known S.purpuratus miRNAs.

Wei Z, Liu X, Feng T, Chang Y. (2011) Novel and Conserved Micrornas in Dalian Purple Urchin (Strongylocentrotus Nudus) Identified by Next Generation Sequencing. Int J Biol Sci 7, 180-192.[article]