title: Genomic analysis of silkworm microRNA promoters and clusters.
abstract: MicroRNAs (miRNAs) are endogenous single-stranded RNAs of 18-22 nt in length, which can regulate the complementary mRNAs at the post-transcriptional level by cleavage or repression of translation of the target mRNAs. Studies have shown that the majority of animal miRNAs are transcribed from independent transcription units, and someare transcribed together with their host genes. However, the nature of the primary transcript of intergenic miRNAs remains unknown. Silkworm (Bombyx mori) miRNAs are representative of those of the Lepidoptera insects and many of them are conserved in Caenorhabditis elegans and other animal species. To date, little is known about the transcriptional regulation of silkworm miRNA genes. We performed the genomic analysis on the silkworm miRNA transcripts around the promoter region including the transcription start site (TSS) and the TATA-box, and on the organization of the miRNA cluster. In 73 pre-miRNAs from the silkworm 131 promoters were detected via a bioinformatics approach. Among them the portion of non-conserved promoters is greater than that of the conserved ones. The genomic organization of pre-miRNAs of the silkworm was globally analyzed and it was determined that 11 of them we reorganized into five clusters. Sequence alignment showed that paralogs existed for some of the miRNAs in the cluster. These results may increase the understanding of the specific sequences upstream of the pre-miRNAs and of the functional implications of miRNA clusters in the silkworm.
authors.affiliation: Jiang Su University of Science and Technology, Zhenjiang City, 212018 Jiangsu Province, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Huang
authors.forename: Xing Jia
authors.initials: XJ
authors.lastname: Shen
authors.forename: Quan
authors.initials: Q
authors.lastname: Zou
authors.forename: Jin Shan
authors.initials: JS
authors.lastname: Huang
authors.forename: Shun Ming
authors.initials: SM
authors.lastname: Tang
mesh_terms: D000818:Animals; D012831:Bombyx / Q000235:genetics*; D019295:Computational Biology; D005786:Gene Expression Regulation / Q000235:genetics; D016678:Genome; D035683:MicroRNAs / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D016385:TATA Box / Q000235:genetics; D024363:Transcription Initiation Site
chemical_list: D035683:MicroRNAs