MicroRNA sequence motifs reveal asymmetry between the stem arms. Export

@article{citeulike:715511, abstract = {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(') and 3(') stemloop precursor arms and we find asymmetry between mature sequences of the 5(') and 3(') stemloop precursor arms. The main observation is that vertebrate organisms have a characteristic motif on the 5(') arm which is in contrast to the 3(') arm motif which mainly show the conserved U at the position of the mature start. Also the vertebrate 5(') arm motif show a semi-conserved G 13 nucleotides upstream from the first position. We compared the 5(') and 3(') arm profiles using the average log likelihood ratio (ALLR) score, as defined by [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(') end where the 5(') arm motif (in contrast to the 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.}, address = {Division of Genetics and Bioinformatics, IBHV and Center for Bioinformatics, The Royal Veterinary and Agricultural University, Gr{\o}nneg\r{a}rdsvej 3, DK-1870 Frederiksberg C, Denmark.}, author = {Gorodkin, J and Havgaard, J H H. and Enster\"{o}, M and Sawera, M and Jensen, P and Ohman, M and Fredholm, M}, citeulike-article-id = {715511}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.compbiolchem.2006.04.006}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16798093}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16798093}, citeulike-linkout-3 = {http://www.sciencedirect.com/science/article/B73G2-4K7NHCX-3/2/b0f30ed356f145081584d5d25b8b64b4}, day = {21}, doi = {10.1016/j.compbiolchem.2006.04.006}, issn = {1476-9271}, journal = {Comput Biol Chem}, keywords = {arms, asymmetry, mirna, precursor, stem}, month = {June}, posted-at = {2006-06-29 11:27:17}, priority = {4}, title = {MicroRNA sequence motifs reveal asymmetry between the stem arms.}, url = {http://dx.doi.org/10.1016/j.compbiolchem.2006.04.006}, year = {2006} }

TY - JOUR ID - citeulike:715511 L3 - citeulike-article-id:715511 N2 - 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(') and 3(') stemloop precursor arms and we find asymmetry between mature sequences of the 5(') and 3(') stemloop precursor arms. The main observation is that vertebrate organisms have a characteristic motif on the 5(') arm which is in contrast to the 3(') arm motif which mainly show the conserved U at the position of the mature start. Also the vertebrate 5(') arm motif show a semi-conserved G 13 nucleotides upstream from the first position. We compared the 5(') and 3(') arm profiles using the average log likelihood ratio (ALLR) score, as defined by [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(') end where the 5(') arm motif (in contrast to the 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. JF - Comput Biol Chem SN - 1476-9271 AD - Division of Genetics and Bioinformatics, IBHV and Center for Bioinformatics, The Royal Veterinary and Agricultural University, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark. TI - MicroRNA sequence motifs reveal asymmetry between the stem arms. KW - arms KW - asymmetry KW - mirna KW - precursor KW - stem AU - Gorodkin, J AU - Havgaard, J H AU - Ensterö, M AU - Sawera, M AU - Jensen, P AU - Ohman, M AU - Fredholm, M PY - 2006/06/21/ UR - http://dx.doi.org/10.1016/j.compbiolchem.2006.04.006 ER -