Full Text:   <1473>

CLC number: Q522

On-line Access: 

Received: 2005-10-08

Revision Accepted: 2006-02-14

Crosschecked: 0000-00-00

Cited: 19

Clicked: 3475

Citations:  Bibtex RefMan EndNote GB/T7714

-   Go to

Article info.
1. Reference List
Open peer comments

Journal of Zhejiang University SCIENCE B 2006 Vol.7 No.10 P.806~816

10.1631/jzus.2006.B0806


Computational prediction of microRNA genes in silkworm genome


Author(s):  TONG Chuan-zhou, JIN Yong-feng, ZHANG Yao-zhou

Affiliation(s):  Institute of Biochemistry, School of Life Science, Zhejiang University, Hangzhou 310029, China; more

Corresponding email(s):   jinyf@zju.edu.cn

Key Words:  miRNA, Silkworm, Computational prediction


TONG Chuan-zhou, JIN Yong-feng, ZHANG Yao-zhou. Computational prediction of microRNA genes in silkworm genome[J]. Journal of Zhejiang University Science B, 2006, 7(10): 806~816.

@article{title="Computational prediction of microRNA genes in silkworm genome",
author="TONG Chuan-zhou, JIN Yong-feng, ZHANG Yao-zhou",
journal="Journal of Zhejiang University Science B",
volume="7",
number="10",
pages="806~816",
year="2006",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.2006.B0806"
}

%0 Journal Article
%T Computational prediction of microRNA genes in silkworm genome
%A TONG Chuan-zhou
%A JIN Yong-feng
%A ZHANG Yao-zhou
%J Journal of Zhejiang University SCIENCE B
%V 7
%N 10
%P 806~816
%@ 1673-1581
%D 2006
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.2006.B0806

TY - JOUR
T1 - Computational prediction of microRNA genes in silkworm genome
A1 - TONG Chuan-zhou
A1 - JIN Yong-feng
A1 - ZHANG Yao-zhou
J0 - Journal of Zhejiang University Science B
VL - 7
IS - 10
SP - 806
EP - 816
%@ 1673-1581
Y1 - 2006
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.2006.B0806


Abstract: 
MicroRNAs (miRNAs) constitute a novel, extensive class of small RNAs (~21 nucleotides), and play important gene-regulation roles during growth and development in various organisms. Here we conducted a homology search to identify homologs of previously validated miRNAs from silkworm genome. We identified 24 potential miRNA genes, and gave each of them a name according to the common criteria. Interestingly, we found that a great number of newly identified miRNAs were conserved in silkworm and Drosophila, and family alignment revealed that miRNA families might possess single nucleotide polymorphisms. miRNA gene clusters and possible functions of complement miRNA pairs are discussed.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

[1] Ambros, V., Bartel, B., Bartel, D.P., Burge, C.B., Carrington, J.C., Chen, X., Dreyfuss, G., Eddy, S.R., Griffiths-Jones, S., Marshall, M., et al., 2003. A uniform system for microRNA annotation. Rna, 9(3):277-279.

[2] Aravin, A.A., Lagos-Quintana, M., Yalcin, A., Zavolan, M., Marks, D., Snyder, B., Gaasterland, T., Meyer, J., Tuschl, T., 2003. The small RNA profile during Drosophila melanogaster development. Dev. Cell, 5(2):337-350.

[3] Banerjee, D., Slack, F., 2002. Control of developmental timing by small temporal RNAs: a paradigm for RNA-mediated regulation of gene expression. Bioessays, 24(2):119-129.

[4] Bartel, D.P., 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116(2):281-297.

[5] Brennecke, J., Hipfner, D.R., Stark, A., Russell, R.B., Cohen, S.M., 2003. Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell, 113(1):25-36.

[6] Gregory, R.I., Chendrimada, T.P., Cooch, N., Shiekhattar, R., 2005. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell, 123(4):631-640.

[7] Hannon, G., 2002. RNA interference. Nature, 418(6894):244-251.

[8] Lagos-Quintana, M., Rauhut, R., Lendeckel, W., Tuschl, T., 2001. Identification of novel genes coding for small expressed RNAs. Science, 294(5543):853-858.

[9] Lagos-Quintana, M., Rauhut, R., Yalcin, A., Meyer, J., Lendeckel, W., Tuschl, T., 2002. Identification of tissue-specific microRNAs from mouse. Curr. Biol., 12(9):735-739.

[10] Lai, E.C., Wiel, C., Rubin, G.M., 2004. Complementary miRNA pairs suggest a regulatory role for miRNA: miRNA duplexes. Rna, 10(2):171-175.

[11] Lau, N.C., Lim, L.P., Weinstein, E.G., Bartel, D.P., 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294(5543):858-862.

[12] Lee, R.C., Ambros, V., 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science, 294(5543):862-864.

[13] Lee, R.C., Feinbaum, R.L., Ambros, V., 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75(5):843-854.

[14] Lee, Y., Jeon, K., Lee, J.T., Kim, S., Kim, V.N., 2002. MicroRNA maturation: stepwise processing and subcellular localization. Embo. J., 21(17):4663-4670.

[15] Lim, L.P., Lau, N.C., Weinstein, E.G., Abdelhakim, A., Yekta, S., Rhoades, M.W., Burge, C.B., Bartel, D.P., 2003. The microRNAs of Caenorhabditis elegans. Genes Dev., 17(8):991-1008.

[16] Llave, C., Kasschau, K.D., Rector, M.A., Carrington, J.C., 2002. Endogenous and silencing-associated small RNAs in plants. Plant Cell, 14(7):1605-1619.

[17] Mourelatos, Z., Dostie, J., Paushkin, S., Sharma, A., Charroux, B., Abel, L., Rappsilber, J., Mann, M., Dreyfuss, G., 2002. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev., 16(6):720-728.

[18] Park, W., Li, J., Song, R., Messing, J., Chen, X., 2002. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA me tabolism in Arabidopsis thaliana. Curr. Biol., 12(17):1484-1495.

[19] Reinhart, B.J., Bartel, D.P., 2002. Small RNAs correspond to centromere heterochromatic repeats. Science, 297(5588):1831.

[20] Reinhart, B.J., Slack, F.J., Basson, M., Pasquinelli, A.E., Bettinger, J.C., Rougvie, A.E., Horvitz, H.R., Ruvkun, G., 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403(6772):901-906.

[21] Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., Bartel, D.P., 2002. MicroRNAs in plants. Genes Dev., 16(13):1616-1626.

[22] Schwarz, D.S., Hutvagner, G., Du, T., Xu, Z., Aronin, N., Zamore, P.D., 2003. Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115(2):199-208.

[23] Seitz, H., Royo, H., Bortolin, M.L., Lin, S.P., Ferguson-Smith, A.C., Cavaille, J., 2004. A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Res., 14(9):1741-1748.

[24] Tanzer, A., Stadler, P.F., 2004. Molecular evolution of a microRNA cluster. J. Mol. Biol., 339(2):327-335.

[25] Xia, Q., Zhou, Z., Lu, C., Cheng, D., Dai, F., Li, B., Zhao, P., Zha, X., Cheng, T., Chai, C., et al., 2004. A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science, 306(5703):1937-1940.

[26] Xu, P., Vernooy, S.Y., Guo, M., Hay, B.A., 2003. The Drosophila microRNA mir-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol., 13(9):790-795.

[27] Zuker, M., 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31(13):3406-3415.

Open peer comments: Debate/Discuss/Question/Opinion

<1>

Please provide your name, email address and a comment





Journal of Zhejiang University-SCIENCE, 38 Zheda Road, Hangzhou 310027, China
Tel: +86-571-87952783; E-mail: cjzhang@zju.edu.cn
Copyright © 2000 - Journal of Zhejiang University-SCIENCE