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Genomic analysis of silkworm microRNA promoters and clusters

  • Genomics. Transcriptomics
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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 some are 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 were organized 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.

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Authors and Affiliations

  1. Jiang Su University of Science and Technology, Zhenjiang City, 212018, Jiangsu Province, China

    Yong Huang, Xing Jia Shen, Jin Shan Huang & Shun Ming Tang

  2. The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang City, 212018, Jiangsu Province, China

    Yong Huang, Xing Jia Shen, Jin Shan Huang & Shun Ming Tang

  3. School of Information Science and Technology of Xiamen University, Xiamen City, 361005, Fujian Province, China

    Quan Zou

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  1. Yong Huang
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  2. Xing Jia Shen
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  4. Jin Shan Huang
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Correspondence to Xing Jia Shen.

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Huang, Y., Shen, X.J., Zou, Q. et al. Genomic analysis of silkworm microRNA promoters and clusters. Mol Biol 45, 197–203 (2011). https://doi.org/10.1134/S0026893310061068

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