Small RNAs Discovered: Contribute to Significant miRBase Update
Non-coding (ncRNAs) are a large class of RNAs which do not encode proteins but possess regulatory functions at the level of translation in cells of various species. There are an increasing amount of data suggesting that there are likely many more ncRNAs that exist, yet to be discovered. Custom small RNA discovery microarrays have been shown to be an effective approach for uncovering novel ncRNAs experimentally and/or to validate predicted candidate ncRNAs.
Recently, researchers at Baylor College of Medicine employed a discovery strategy of computational prediction and microarray expression profiling to uncover a large number of novel small RNAs in embryonic stem (ES) cells. Dr. Preethi Gunaratne and co-workers reported using computation, custom small RNA microarray from LC Sciences, and validation experiments to uncover hundreds of novel small RNAs in ES cells. These small non-coding RNAs (ncRNAs) were from adult tissue progenitor transcript sequences and are micro-conserved elements. The detection probes were designed for custom array synthesis by LC Sciences and included the standard microRNA (miRNA) sequences in miRBase, a comprehensive panel of 2,617 micro-conserved ncRNA sequences, and several hundreds of literature reported small RNAs or miRNAs. Two generations of custom array designs were used for optimizing the probes. These profiling studies using ES cell lines as well as normal adult mouse tissues identified 545 small RNAs that are enriched in ES cells over adult cells. Of these, more than 100 exhibited down-regulation in ES gene-knockout cells typical of miRNA.
In a similar way, LC Sciences’ custom small RNA arrays have provided means for validation of computational predictions of Bombyx mori (silkworm) and Solanum lycopersicum (Tomato) miRNAs. These are species whose genomes are incomplete at the present time. It is well known that miRNAs are important players for regulation of cellular activities. Therefore, the establishment of miRNAs in these traditional industrial or agricultural important species should lead to better understanding of the fundamentals of their growth, maturation, and disease resistance.
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