MicroRNA sequence motifs reveal asymmetry between the stem arms

The processing of micro RNAs (miRNAs) from their stemloop precursor have revealed asymmetry in the processing of the mature and its star sequence. Furthermore, the miRNA processing system between organism differ. To assess this at the sequence level we have investigated mature miRNAs in their genomic contexts. We have compared profiles of mature miRNAs within their genomic context of the 5′5′ and 3′3′ stemloop precursor arms and we find asymmetry between mature sequences of the 5′5′ and 3′3′ stemloop precursor arms. The main observation is that vertebrate organisms have a characteristic motif on the 5′5′ arm which is in contrast to the 3′3′ arm motif which mainly show the conserved U at the position of the mature start. Also the vertebrate 5′5′ arm motif show a semi-conserved G 13 nucleotides upstream from the first position. We compared the 5′5′ and 3′3′ arm profiles using the average log likelihood ratio (ALLR) score, as defined by Wang and Stormo (2003) [Wang T., Stormo, G.D., 2003. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 2369–2380.] and computing a p  -value we find that the two profiles differs significantly in their 3′3′ end where the 5′5′ arm motif (in contrast to the 3′3′ arm motif) has a semi-conserved GU rich region. Similar findings are also obtained for other organisms, such as fly, worm and plants. The observed similarities and differences between closely and distantly related organisms are discussed and related to current knowledge of miRNA processing.