tailieunhanh - Báo cáo khoa học: Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes

MicroRNAs (miRNAs) have been proven to play important roles at the post-transcriptional level in animals and plants. To investigate clustering patterns and specific sequence characteristics in the flanking regions of plant miRNA genes, we performed genome-wide analyses ofArabidopsis thaliana, Populus trichocarpa, Oryza sativaand Sorghum bicolor. | IFEBS Journal Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes Meng Zhou1 z Jie Sun1 z Qiang-Hu Wang1 z Li-Qun Song2 Guang Zhao1 Hong-Zhi Wang2 Hai-Xiu Yang1 and Xia Li1 1 College of Bioinformatics Science and Technology Harbin MedicalUniversity Harbin China 2 Department of InternalMedicine Affiliated Hospitalof Heilongjiang University of Chinese Medicine Harbin China Keywords clustering patterns flanking regions motif plant microRNA gene sequence characteristics Correspondence Xia Li College of Bioinformatics Science and Technology Harbin MedicalUniversity Harbin 150081 China. Fax 86 045186615922 Tel 86 045186669617 E-mail lixia@ These authors contributed equally to this work Received 11 October 2010 revised 7 December 2010 accepted 7 January 2011 doi MicroRNAs miRNAs have been proven to play important roles at the post-transcriptional level in animals and plants. To investigate clustering patterns and specific sequence characteristics in the flanking regions of plant miRNA genes we performed genome-wide analyses of Arabidopsis thaliana Populus trichocarpa Oryza sativa and Sorghum bicolor. Our results showed that miRNA pair distances were significantly higher than would have been expected to occur at random and that the number of miRNA gene pairs separated by very short distances of 1 kb was higher than of protein-coding gene pairs. Analysis of the promoter architecture of different miRNA genes in plants revealed significant differences in the number and distribution of core promoters between intergenic miRNAs and intragenic miRNAs and between highly conserved miRNAs and low conserved or nonconserved miRNAs. We applied two motif-finding algorithms to search for over-represented statistically significant sequence motifs and discovered six species-specific motifs across the four plant species studied. Moreover we also identified for the first time several significantly .