Computational Identification of MicroRNAs and their Targets in two Species of Evergreen Spruce Tree (Picea)
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.
[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.
[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.
@article{"International Journal of Biological, Life and Agricultural Sciences:52089", author = "Muhammad Y.K. Barozai and Ifthikhar A. Baloch and M. Din", title = "Computational Identification of MicroRNAs and their Targets in two Species of Evergreen Spruce Tree (Picea)", 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", volume = "5", number = "3", pages = "128-6", }
