Computational Identification of MicroRNAs and their Targets in two Species of Evergreen Spruce Tree (Picea)

Authors: Muhammad Y.K. Barozai, Ifthikhar A. Baloch, M. Din

Abstract:

MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs about 20 to 24 nucleotides long. Their conserved nature among the various organisms makes them a good source of new miRNAs discovery by comparative genomics approach. The study resulted in 21 miRNAs of 20 pre-miRNAs belonging to 16 families (miR156, 157, 158, 164, 165, 168, 169, 172, 319, 390, 393, 394, 395, 400, 472 and 861) in evergreen spruce tree (Picea). The miRNA families; miR 157, 158, 164, 165, 168, 169, 319, 390, 393, 394, 400, 472 and 861 are reported for the first time in the Picea. All 20 miRNA precursors form stable minimum free energy stem-loop structure as their orthologues form in Arabidopsis and the mature miRNA reside in the stem portion of the stem loop structure. Sixteen (16) miRNAs are from Picea glauca and five (5) belong to Picea sitchensis. Their targets consist of transcription factors, growth related, stressed related and hypothetical proteins.

Keywords: BLAST, Comparative Genomics, Micro-RNAs, Spruce

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1058241

References:

[1] Sunset Western Garden Book, (1995): 606-607.
[2] Sigurgeirsson, A. and Szmidt, A. E. Phylogenetic and biogeographic implications of chloroplast DNA variation in Picea. Nordic Journal of Botany 13(3): (1993) 233-246.
[3] Mica E., Gianfranceschi L. and Pe M. E., Characterization of five microRNA families in maize. J. Expl. Bot. 57(11): (2006) 2601-2612.
[4] Bonnet E., Wuyts J., Rouze P. and Van-de-Peer Y. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. PNAS USA. 101: (2004) 11511-11516.
[5] Weber M.J. New human and mouse microRNA genes found by homology search. FEBS J.272: (2005) 59-73.
[6] Bartel D. P. MicroRNAs: genomics, biogenesis, mechanism, and function.Cell.116: (2004) 281-297.
[7] Carrington J.C. and Ambros V. Role of microRNAs in plant and animal development. Sci. 301: (2003) 336-338.
[8] Hammond S. C., Bernstein E., Beach D .and Hannon G.J. An RNAdirected nuclease mediatesposttranscriptional gene silencing in Drosophila cells. Nat. 404: (2000) 293-296.
[9] KuriharaY. and Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1protein functions. PNAS USA.101: (2004) 12753- 12758.
[10] Aukerman M. J. and Sakai H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-Like target genes.Plant Cell.15: (2003) 2730-2741.
[11] Tang G., Reinhart B. J., Bartel D. P. and Zamore P .D. A biochemical framework for RNA silencing in plants. Genes Dev. 17: (2003) 49-63.
[12] Novina C. D. and Sharp P.A.The RNAi revolution. Nat. 430: (2004) 161-164.
[13] Kidner C. A and Martienssen R. A. The developmental role of microRNA in plants .Curr Opin Plant Biol.8: (2005) 38-44.
[14] Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Sci. 303: (2003) 2022-2025.
[15] Allen E., Xie Z., Gustafson A. M., and Carrington J. C., microRNAdirected phasing during transacting siRNA biogenesis in plants. Cell. 121: (2005) 207-221.
[16] Yoshikawa M., Peragine A., Park M. Y. and Poethig R. S., A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes & Dev. 19: (2005) 2164-2175.
[17] Lu S., Sun Y. H., Shi R., Clark C., Li L. and Chiang V. L. Novel and mechanical stress responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. The PlantCell.17: (2005) 2186-2203.
[18] Sunkar R. and Zhu J. K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis.The Plant Cell.16: (2004) 2001- 2019.
[19] Johnson S. M., Grosshansm H., Shingara J., Byrom M., Jarvis R., Cheng A., Labourier E., Reinert K. L., Brown D. and Slack F.J. RAS is regulated by the let-7 microRNA family.Cell.120(5): (2005) 635-647.
[20] Bennasser Y., Le S.Y., Yeung M. L. and Jeang K. T., HIV-1 encoded candidate micro-RNAs and their cellular targets. Retro viro.1(1):(2004) 43.
[21] Reinhart B. J., Weinstein E. G., Rhoades M. W., Bartel B. and Bartel D. P. MicroRNAs in plants. Genes Dev. 16: (2002) 1616-1626.
[22] Mario A.V., Juan C.P. and Jean-Philippe V.C. A Family of MicroRNAs Present in Plants and Animals. Plant Cell.18: (2006) 3355-3369.
[23] Barozai M.Y.K., Irfan M., Yousaf R., Ali I., Qaisar U., Maqbool A., Zahoor M., Rashid B., Hussnain T., and Riazuddin S. Identification of micro-RNAs in cotton. Plant Physiol and Biochem. 46 (8-9): (2008) 739-51.
[24] Zhang B., Pan X., Cannon C. H., Cobb G. P. and Anderson T.A., Conservation and divergence ofplant microRNA genes. The Plant J. 46: (2006) 243-259.
[25] Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res. 32D: (2004) 109-111.
[26] Altschul S. F. Gish W., Miller W., Myers E.W. and Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 215: (1990) 403-410.
[27] Stephen F. A., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W. and Lipman D. J. Gapped BLAST and PSI-BLAST, A new generation of protein database search programs. Nucleic Acids Res. 25: (1997) 3389-3402.
[28] Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: (2003) 3406-3415.
[29] Li S. C., Pan C.U. and Lin W.C. Bioinformatic discovery of microRNA precursors from human ESTs and introns. BMC Gen. 7: (2006) 164.
[30] Crooks G.E., Hon G., Chandonia J. M., Brenner S.E. WebLogo: A sequence logo generator, Gen. Res. 14: (2004)1188-1190.
[31] Kruger J and Rehmsmeier M. RNA hybrid: microRNA target prediction easy, fast and flexible Nucl. Acids. Res., 34(2): (2006) 451-454.
[32] Zhang B. H., PanX. P., WangQ. L., CobbG. P., Todd A. A. Identification and characterization of new plant microRNAs using EST analysis. Cell Research, 15(5): (2005) 336-360.
[33] Yakovlev I. A., Fossdal C. G., Johnsen O. MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce. New Phytol. 187: (2010) 1154-1169.
[34] Ambros V., Bartel B. and Bartel D. P. A uniform system for microRNA annotation. RNA. 9: (2003) 277-279.
[35] Meyers B. C., Axtell M. J., Bartel B., et al. Criteria for Annotation of Plant MicroRNAs. The Plant Cell. 20: (2008) 3186-3190.
[36] Aili L., and Long M. Evolution of plant microRNA gene families Cell Research 17: (2007)212-218.