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Novel microRNAs in silkworm (Bombyx mori)

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Abstract

We acquired more than 4 million useful sequences using a high-throughput method from a library for miRNA identification, which is constructed from a mixture of 14 RNA samples from different developmental stages. We mapped 247,410 reads to known silkworm miRNAs in miRBase (13.0), 701,913 reads to other RNA molecules based on sequence homology, and 3,219,395 reads to the silkworm genome. Our analysis identified 54 silkworm known miRNAs. A striking strand bias between miRNAs and their corresponding miRNA*s was found, and was speculated to reflect that transcripts from the passenger strand of pre-miRNAs may have important biological roles. Using an elaborate screening protocol, we predicted 287 candidate novel miRNAs (represent 116,494 short reads), and 59 of them have both miRNA and miRNA* sequences. Most of the previously identified silkworm miRNAs are cross-species conserved with a high abundance, while those predicted candidates tend to be species-specific miRNAs. Our discovery of SNPs among miRNAs implied within-species functional diversity. Target prediction uncovers that considerable silkworm miRNAs may aim at modulating more than one hormone signaling pathway components and/or hormone biosynthesis-related proteins implying their important roles in silkworm development.

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Reference

  • Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T (2003) A uniform system for microRNA annotation. RNA 9:277–279

    Article  CAS  PubMed  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  CAS  PubMed  Google Scholar 

  • Baskerville S, Bartel DP (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11:241–247

    Article  CAS  PubMed  Google Scholar 

  • Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33:e179

    Article  PubMed  Google Scholar 

  • Chin LJ, Ratner E, Leng S, Zhai R, Nallur S, Babar I, Muller RU, Straka E, Su L, Burki EA, Crowell RE, Patel R, Kulkarni T, Homer R, Zelterman D, Kidd KK, Zhu Y, Christiani DC, Belinsky SA, Slack FJ, Weidhaas JB (2008) A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk. Cancer Res 68:8535–8540

    Article  CAS  PubMed  Google Scholar 

  • Cruz J, Martin D, Belles X (2007) Redundant ecdysis regulatory functions of three nuclear receptor HR3 isoforms in the direct-developing insect Blattella germanica. Mech Dev 124:180–189

    Article  CAS  PubMed  Google Scholar 

  • Davison TS, Johnson CD, Andruss BF (2006) Analyzing micro-RNA expression using microarrays. Methods Enzymol 411:14–34

    Article  CAS  PubMed  Google Scholar 

  • Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ (2004) Processing of primary microRNAs by the Microprocessor complex. Nature 432:231–235

    Article  CAS  PubMed  Google Scholar 

  • Denman RB (1993) Using RNAFOLD to predict the activity of small catalytic RNAs. Biotechniques 15:1090–1095

    CAS  PubMed  Google Scholar 

  • Duan R, Pak C, Jin P (2007) Single nucleotide polymorphism associated with mature miR-125a alters the processing of pri-miRNA. Hum Mol Genet 16:1124–1131

    Article  CAS  PubMed  Google Scholar 

  • Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS (2003) MicroRNA targets in Drosophila. Genome Biol 5:R1

    Article  PubMed  Google Scholar 

  • Eystathioy T, Swevers L, Iatrou K (2001) The orphan nuclear receptor BmHR3A of Bombyx mori: hormonal control, ovarian expression and functional properties. Mech Dev 103:107–115

    Article  CAS  PubMed  Google Scholar 

  • Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2:e219

    Article  PubMed  Google Scholar 

  • Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, Montgomery TA, Gilbert SD, Dasenko M, Backman TW, Givan SA, Carrington JC (2009) Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 15:992–1002

    Article  CAS  PubMed  Google Scholar 

  • Goff LA, Davila J, Swerdel MR, Moore JC, Cohen RI, Wu H, Sun YE, Hart RP (2009) Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic stem cells and neural precursors. PLoS One 4:e7192

    Article  PubMed  Google Scholar 

  • Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432:235–240

    Article  CAS  PubMed  Google Scholar 

  • Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–158

    Article  CAS  PubMed  Google Scholar 

  • Horikawa Y, Wood CG, Yang H, Zhao H, Ye Y, Gu J, Lin J, Habuchi T, Wu X (2008) Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Clin Cancer Res 14:7956–7962

    Article  CAS  PubMed  Google Scholar 

  • Horike N, Sonobe H (1999) Ecdysone 20-monooxygenase in eggs of the silkworm, Bombyx mori: enzymatic properties and developmental changes. Arch Insect Biochem Physiol 41:9–17

    Article  CAS  PubMed  Google Scholar 

  • Hu Z, Chen J, Tian T, Zhou X, Gu H, Xu L, Zeng Y, Miao R, Jin G, Ma H, Chen Y, Shen H (2008) Genetic variants of miRNA sequences and non-small cell lung cancer survival. J Clin Invest 118:2600–2608

    Article  CAS  PubMed  Google Scholar 

  • Jazdzewski K, Liyanarachchi S, Swierniak M, Pachucki J, Ringel MD, Jarzab B, de la Chapelle A (2009) Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer. Proc Natl Acad Sci U S A 106:1502–1505

    Article  CAS  PubMed  Google Scholar 

  • John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS (2004) Human MicroRNA targets. PLoS Biol 2:e363

    Article  PubMed  Google Scholar 

  • Kato M, de Lencastre A, Pincus Z, Slack FJ (2009) Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during C. elegans development. Genome Biol 10:R54

    Article  PubMed  Google Scholar 

  • Kim VN (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6:376–385

    Article  CAS  PubMed  Google Scholar 

  • Kim S, Lee UJ, Kim MN, Lee EJ, Kim JY, Lee MY, Choung S, Kim YJ, Choi YC (2008) MicroRNA miR-199a* regulates the MET proto-oncogene and the downstream extracellular signal-regulated kinase 2 (ERK2). J Biol Chem 283:18158–18166

    Article  CAS  PubMed  Google Scholar 

  • Kim YK, Yu J, Han TS, Park SY, Namkoong B, Kim DH, Hur K, Yoo MW, Lee HJ, Yang HK, Kim VN (2009) Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer. Nucleic Acids Res 37:1672–1681

    Article  CAS  PubMed  Google Scholar 

  • Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23:4051–4060

    Article  CAS  PubMed  Google Scholar 

  • Lehmussola A, Ruusuvuori P, Yli-Harja O (2006) Evaluating the performance of microarray segmentation algorithms. Bioinformatics 22:2910–2917

    Article  CAS  PubMed  Google Scholar 

  • Leung WS, Lin MC, Cheung DW, Yiu SM (2008) Filtering of false positive microRNA candidates by a clustering-based approach. BMC Bioinformatics 9(Suppl 12):S3

    Article  PubMed  Google Scholar 

  • Liu S, Xia Q, Zhao P, Cheng T, Hong K, Xiang Z (2007) Characterization and expression patterns of let-7 microRNA in the silkworm (Bombyx mori). BMC Dev Biol 7:88

    Article  PubMed  Google Scholar 

  • Niwa R, Niimi T, Honda N, Yoshiyama M, Itoyama K, Kataoka H, Shinoda T (2008) Juvenile hormone acid O-methyltransferase in Drosophila melanogaster. Insect Biochem Mol Biol 38:714–720

    Article  CAS  PubMed  Google Scholar 

  • Ohman M (2007) A-to-I editing challenger or ally to the microRNA process. Biochimie 89:1171–1176

    Article  CAS  PubMed  Google Scholar 

  • Okamura K, Phillips MD, Tyler DM, Duan H, Chou YT, Lai EC (2008) The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nat Struct Mol Biol 15:354–363

    Article  CAS  PubMed  Google Scholar 

  • Oulas A, Boutla A, Gkirtzou K, Reczko M, Kalantidis K, Poirazi P (2009) Prediction of novel microRNA genes in cancer-associated genomic regions—a combined computational and experimental approach. Nucleic Acids Res 37:3276–87

    Article  CAS  PubMed  Google Scholar 

  • Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193–1207

    Article  CAS  PubMed  Google Scholar 

  • Schickel R, Boyerinas B, Park SM, Peter ME (2008) MicroRNAs: key players in the immune system, differentiation, tumorigenesis and cell death. Oncogene 27:5959–5974

    Article  CAS  PubMed  Google Scholar 

  • Sempere LF, Dubrovsky EB, Dubrovskaya VA, Berger EM, Ambros V (2002) The expression of the let-7 small regulatory RNA is controlled by ecdysone during metamorphosis in Drosophila melanogaster. Dev Biol 244:170–179

    Article  CAS  PubMed  Google Scholar 

  • Sempere LF, Sokol NS, Dubrovsky EB, Berger EM, Ambros V (2003) Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-Complex gene activity. Dev Biol 259:9–18

    Article  CAS  PubMed  Google Scholar 

  • Sun G, Yan J, Noltner K, Feng J, Li H, Sarkis DA, Sommer SS, Rossi JJ (2009) SNPs in human miRNA genes affect biogenesis and function. RNA 15:1640–51

    Article  CAS  PubMed  Google Scholar 

  • Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK (2008) Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 8:25

    Article  PubMed  Google Scholar 

  • Sutherland JD, Kozlova T, Tzertzinis G, Kafatos FC (1995) Drosophila hormone receptor 38: a second partner for Drosophila USP suggests an unexpected role for nuclear receptors of the nerve growth factor-induced protein B type. Proc Natl Acad Sci U S A 92:7966–7970

    Article  CAS  PubMed  Google Scholar 

  • T Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen JT (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 36:e141

    Article  Google Scholar 

  • Wang Y, Stricker HM, Gou D, Liu L (2007) MicroRNA: past and present. Front Biosci 12:2316–2329

    Article  CAS  PubMed  Google Scholar 

  • Wieczorek E, Parkitna JM, Szkudlarek J, Ozyhar A, Kochman M (1996) Immunoaffinity purification of juvenile hormone-binding protein from Galleria mellonella hemolymph. Acta Biochim Pol 43:603–610

    CAS  PubMed  Google Scholar 

  • Xia Q, Zhou Z, Lu C, Cheng D, Dai F, Li B, Zhao P, Zha X, Cheng T, Chai C, Pan G, Xu J, Liu C, Lin Y, Qian J, Hou Y, Wu Z, Li G, Pan M, Li C, Shen Y, Lan X, Yuan L, Li T, Xu H, Yang G, Wan Y, Zhu Y, Yu M, Shen W, Wu D, Xiang Z, Yu J, Wang J, Li R, Shi J, Li H, Su J, Wang X, Zhang Z, Wu Q, Li J, Zhang Q, Wei N, Sun H, Dong L, Liu D, Zhao S, Zhao X, Meng Q, Lan F, Huang X, Li Y, Fang L, Li D, Sun Y, Yang Z, Huang Y, Xi Y, Qi Q, He D, Huang H, Zhang X, Wang Z, Li W, Cao Y, Yu Y, Yu H, Ye J, Chen H, Zhou Y, Liu B, Ji H, Li S, Ni P, Zhang J, Zhang Y, Zheng H, Mao B, Wang W, Ye C, Wong GK, Yang H (2004) A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 306:1937–1940

    Article  PubMed  Google Scholar 

  • Xia Q et al (2008) The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem Mol Biol 38:1036–1045

    Article  Google Scholar 

  • Yin JQ, Zhao RC, Morris KV (2008) Profiling microRNA expression with microarrays. Trends Biotechnol 26:70–76

    Article  CAS  PubMed  Google Scholar 

  • Yu X, Zhou Q, Cai Y, Luo Q, Lin H, Hu S, Yu J (2009) A discovery of novel microRNAs in the silkworm (Bombyx mori) genome. Genomics 94:438–444

    Article  CAS  PubMed  Google Scholar 

  • Yu X, Zhou Q, Li SC, Luo Q, Cai Y, Lin WC, Chen H, Yang Y, Hu S, Yu J (2008) The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stages. PLoS ONE 3:e2997

    Article  PubMed  Google Scholar 

  • Zhang Y, Zhou X, Ge X, Jiang J, Li M, Jia S, Yang X, Kan Y, Miao X, Zhao G, Li F, Huang Y (2009) Insect-specific microRNA involved in the development of the silkworm Bombyx mori. PLoS One 4:e4677

    Article  PubMed  Google Scholar 

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Acknowledgments

We would like to thank Professor Anying Xu of the Sericultural Research Institute, Chinese Academy of Agricultural Sciences, for providing silkworm eggs. We are especially grateful for the support of bioinformatics analysis from Jiandong Sun (Life Technologies, Inc.). This work was supported by the Knowledge Innovation Program of the Chinese Academy of Sciences (08SQN01185) awarded to Xiaomin Yu, and a grant from the Ministry of Science and Technology(2006CB910400) awarded to Jun Yu.

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Authors and Affiliations

  1. Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China

    Yimei Cai, Xiaomin Yu, Qing Zhou, Caixia Yu, Haiyan Hu, Jiucheng Liu, Hongbin Lin, Jin Yang, Bing Zhang, Peng Cui, Songnian Hu & Jun Yu

  2. Graduate School of Chinese Academy of Sciences, Beijing, 100039, China

    Yimei Cai, Haiyan Hu & Jiucheng Liu

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  1. Yimei Cai
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  2. Xiaomin Yu
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  3. Qing Zhou
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  11. Songnian Hu
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  12. Jun Yu
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Corresponding authors

Correspondence to Songnian Hu or Jun Yu.

Additional information

Yimei Cai, Xiaomin Yu, and Qing Zhou contributed equally to this work.

Electronic supplementary materials

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Supplemental file S1

Designed stem-loop RT PCR primers. (XLS 35 kb) (XLS 35 kb)

Supplemental file S2

Data processing pipeline. (GIF 19 kb)

High resolution image (TIFF 176 kb)

Supplemental file S3

Overlaps with published miRNA data. (DOC 45 kb) (DOC 45 kb)

Supplemental file S4

List of silkworm candidate novel miRNAs without stars. (XLS 46 kb) (XLS 46 kb)

Supplemental file S5

Candidate novel silkworm miRNA hairpin structures. (TXT 94 kb) (TXT 94 kb)

Supplemental file S6

Cross-species conserved candidate novel miRNAs in other insects. (XLS 69 kb) (XLS 69 kb)

Supplemental file S7

Genome location of the pre-miRNA sequences. (XLS 97 kb) (XLS 97 kb)

Supplemental file S8

Predicated targets with species conservation. (XLS 96 kb) (XLS 96 kb)

ESM Table 1

Details about known silkworm miRNAs identified by SOLiD sequencing. (DOC 100 kb)

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Cai, Y., Yu, X., Zhou, Q. et al. Novel microRNAs in silkworm (Bombyx mori). Funct Integr Genomics 10, 405–415 (2010). https://doi.org/10.1007/s10142-010-0162-7

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  • DOI: https://doi.org/10.1007/s10142-010-0162-7

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