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CLC number: S562

On-line Access: 2024-08-27

Received: 2023-10-17

Revision Accepted: 2024-05-08

Crosschecked: 2015-03-18

Cited: 5

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Citations:  Bibtex RefMan EndNote GB/T7714

 ORCID:

Jun Ma

http://orcid.org/0000-0003-4354-2523

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Journal of Zhejiang University SCIENCE B 2015 Vol.16 No.4 P.296-303

http://doi.org/10.1631/jzus.B1400277


Expression profiles of miRNAs in Gossypium raimondii


Author(s):  Jun Ma, Teng-long Guo, Qing-lian Wang, Kun-bo Wang, Run-run Sun, Bao-hong Zhang

Affiliation(s):  Department of Biology, East Carolina University, Greenville, NC 27858, USA; more

Corresponding email(s):   zhangb@ecu.edu

Key Words:  Cotton, miRNA, Expression profiles, Quantitative real-time PCR (qRT-PCR), Gossypium raimondii


Jun Ma, Teng-long Guo, Qing-lian Wang, Kun-bo Wang, Run-run Sun, Bao-hong Zhang. Expression profiles of miRNAs in Gossypium raimondii[J]. Journal of Zhejiang University Science B, 2015, 16(4): 296-303.

@article{title="Expression profiles of miRNAs in Gossypium raimondii",
author="Jun Ma, Teng-long Guo, Qing-lian Wang, Kun-bo Wang, Run-run Sun, Bao-hong Zhang",
journal="Journal of Zhejiang University Science B",
volume="16",
number="4",
pages="296-303",
year="2015",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B1400277"
}

%0 Journal Article
%T Expression profiles of miRNAs in Gossypium raimondii
%A Jun Ma
%A Teng-long Guo
%A Qing-lian Wang
%A Kun-bo Wang
%A Run-run Sun
%A Bao-hong Zhang
%J Journal of Zhejiang University SCIENCE B
%V 16
%N 4
%P 296-303
%@ 1673-1581
%D 2015
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1400277

TY - JOUR
T1 - Expression profiles of miRNAs in Gossypium raimondii
A1 - Jun Ma
A1 - Teng-long Guo
A1 - Qing-lian Wang
A1 - Kun-bo Wang
A1 - Run-run Sun
A1 - Bao-hong Zhang
J0 - Journal of Zhejiang University Science B
VL - 16
IS - 4
SP - 296
EP - 303
%@ 1673-1581
Y1 - 2015
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B1400277


Abstract: 
miRNAs are a class of conserved, small, endogenous, and non-protein-coding RNA molecules with 20–24 nucleotides (nt) in length that function as post-transcriptional modulators of gene expression in eukaryotic cells. Functional studies have demonstrated that plant miRNAs are involved in the regulation of a wide range of plant developmental processes. To date, however, no research has been carried out to study the expression profiles of miRNAs in Gossypium raimondii, a model cotton species. We selected 16 miRNAs to profile their tissue-specific expression patterns in G. raimondii four different tissues, and these miRNAs are reported to play important roles in plant growth and development. Our results showed that the expression levels of these miRNAs varied significantly from one to another in a tissue-dependent manner. Eight miRNAs, including miR-159, miR-162, miR-164, miR-172, miR-390, miR-395, miR-397, and miR-398, exhibited exclusively high expression levels in flower buds, suggesting that these miRNAs may play significant roles in floral development. The expression level of miR-164 was relatively high in shoots beside flower buds, implying that the function of miR-164 is not only limited to floral development but it may also play an important role in shoot development. Certain miRNAs such as miR-166 and miR-160 were extremely highly expressed in all of the four tissues tested compared with other miRNAs investigated, suggesting that they may play regulatory roles at multiple development stages. This study will contribute to future studies on the functional characterization of miRNAs in cotton.

MicroRNA 在雷蒙德氏棉中的表达

中文概要:
目的:探索16个保守microRNA在雷蒙德氏棉中的表达情况。
创新点:首次研究了microRNA在雷蒙德氏棉四个组织的表达情况。
方法:设计16个microRNA的引物,并提取雷蒙德氏棉四个不同组织的RNA进行实时荧光定量聚合酶链式反应(qRT-PCR)。
结论:在不同的组织中,这些microRNA 的表达水平差异很大。包括miR-159、miR-162、miR-164、miR-172、miR-390、miR-395、miR-397和miR-398在内的8个microRNA在花蕾中表达含量非常 高,而另外一些microRNA,例如miR-166和miR-160,在四个不同组织中都有很高的表达量。

关键词:棉花;microRNA;表达谱;实时荧光定量聚合酶链式反应(qRT-PCR);雷蒙德氏棉

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

Reference

[1]Achard, P., Herr, A., Baulcombe, D.C., et al., 2004. Modulation of floral development by a gibberellin-regulated microRNA. Development, 131(14):3357-3365.

[2]Aida, M., Tasaka, M., 2006. Genetic control of shoot organ boundaries. Curr. Opin. Plant Biol., 9(1):72-77.

[3]Aukerman, M.J., Sakai, H., 2003. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell, 15(11):2730-2741.

[4]Bao, N., Lye, K.W., Barton, M.K., 2004. MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Dev. Cell, 7(5):653-662.

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

[6]Bowman, J.L., 2004. Class III HD-Zip gene regulation, the golden fleece of ARGONAUTE activity? Bioessays, 26(9):938-942.

[7]Carrington, J.C., Ambros, V., 2003. Role of microRNAs in plant and animal development. Science, 301(5631):336-338.

[8]Chen, X.M., 2004. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 303(5666):2022-2025.

[9]Emery, J.F., Floyd, S.K., Alvarez, J., et al., 2003. Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr. Biol., 13(20):1768-1774.

[10]Endo, Y., Iwakawa, H.O., Tomari, Y., 2013. Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly. EMBO Rep., 14(7):652-658.

[11]Fahlgren, N., Montgomery, T.A., Howell, M.D., et al., 2006. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr. Biol., 16(9):939-944.

[12]Garcia, D., 2008. A miRacle in plant development: role of microRNAs in cell differentiation and patterning. Semin. Cell Dev. Biol., 19(6):586-595.

[13]Gocal, G.F., Sheldon, C.C., Gubler, F., et al., 2001. GAMYB-like genes, flowering, and gibberellin signaling in Arabidopsis. Plant Physiol., 127(4):1682-1693.

[14]Gong, L., Kakrana, A., Arikit, S., et al., 2013. Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species. Genome Biol. Evol., 5(12):2449-2459.

[15]Guo, H.S., Xie, Q., Fei, J.F., et al., 2005. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell, 17(5):1376-1386.

[16]Juarez, M.T., Kui, J.S., Thomas, J., et al., 2004. MicroRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature, 428(6978):84-88.

[17]Jung, J.H., Park, C.M., 2007. miR166/165 genes exhibit dynamic expression patterns in regulating shoot apical meristem and floral development in Arabidopsis. Planta, 225(6):1327-1338.

[18]Kaneko, M., Inukai, Y., Ueguchi-Tanaka, M., et al., 2004. Loss-of-function mutations of the rice GAMYB gene impair α-amylase expression in aleurone and flower development. Plant Cell, 16(1):33-44.

[19]Kim, J., Jung, J.H., Reyes, J.L., et al., 2005. MicroRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J., 42(1):84-94.

[20]Kurihara, Y., Watanabe, Y., 2004. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. PNAS, 101(34):12753-12758.

[21]Laufs, P., Peaucelle, A., Morin, H., et al., 2004. MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development, 131(17):4311-4322.

[22]Lauter, N., Kampani, A., Carlson, S., et al., 2005. MicroRNA172 down-regulates glossy15 to promote vegetative phase change in maize. PNAS, 102(26):9412-9417.

[23]Lee, Y., Kim, M., Han, J., et al., 2004. MicroRNA genes are transcribed by RNA polymerase II. EMBO J., 23(20):4051-4060.

[24]Liu, N., Tu, L., Tang, W., et al., 2014. Small RNA and degradome profiling reveals a role for miRNAs and their targets in the developing fibers of Gossypium barbadense. Plant J., 80(2):331-344

[25]Ma, J., Wang, Q., Sun, R., et al., 2014. Genome-wide identification and expression analysis of TCP transcription factors in Gossypium raimondii. Sci. Rep., 4:6645.

[26]Mallory, A.C., Dugas, D.V., Bartel, D.P., et al., 2004. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr. Biol., 14(12):1035-1046.

[27]McConnell, J.R., Emery, J., Eshed, Y., et al., 2001. Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. Nature, 411(6838):709-713.

[28]Millar, A.A., Gubler, F., 2005. The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell, 17(3):705-721.

[29]Millar, A.A., Waterhouse, P.M., 2005. Plant and animal microRNAs: similarities and differences. Funct. Integr. Genomics, 5(3):129-135.

[30]Montgomery, T.A., Howell, M.D., Cuperus, J.T., et al., 2008. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell, 133(1):128-141.

[31]Ohashi-Ito, K., Fukuda, H., 2003. HD-Zip III homeobox genes that include a novel member, ZeHB-13 (Zinnia)/ATHB-15 (Arabidopsis), are involved in procambium and xylem cell differentiation. Plant Cell Physiol., 44(12):1350-1358.

[32]Otsuga, D., Deguzman, B., Prigge, M.J., et al., 2001. REVOLUTA regulates meristem initiation at lateral positions. Plant J., 25(2):223-236.

[33]Papp, I., Mette, M.F., Aufsatz, W., et al., 2003. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol., 132(3):1382-1390.

[34]Park, M.Y., Wu, G., Gonzalez-Sulser, A., et al., 2005. Nuclear processing and export of microRNAs in Arabidopsis. PNAS, 102(10):3691-3696.

[35]Prigge, M.J., Otsuga, D., Alonso, J.M., et al., 2005. Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. Plant Cell, 17(1):61-76.

[36]Rhoades, M.W., Reinhart, B.J., Lim, L.P., et al., 2002. Prediction of plant microRNA targets. Cell, 110(4):513-520.

[37]Rubio-Somoza, I., Weigel, D., 2011. MicroRNA networks and developmental plasticity in plants. Trends Plant Sci., 16(5):258-264.

[38]Sieber, P., Wellmer, F., Gheyselinck, J., et al., 2007. Redundancy and specialization among plant microRNAs: role of the MIR164 family in developmental robustness. Development, 134(6):1051-1060.

[39]Xie, F.L., Jones, D.C., Wang, Q.L., et al., 2015. Small RNA sequencing identifies miRNA roles in ovule and fiber development. Plant Biotechnol. J., 13(3):338-352.

[40]Xu, L., Yang, L., Huang, H., 2007. Transcriptional, post-transcriptional and post-translational regulations of gene expression during leaf polarity formation. Cell Res., 17(6):512-519.

[41]Xue, W., Wang, Z., Du, M., et al., 2013. Genome-wide analysis of small RNAs reveals eight fiber elongation-related and 257 novel microRNAs in elongating cotton fiber cells. BMC Genomics, 14:629.

[42]Zhang, B.H., 2015. MicroRNA: a new target for improving plant tolerance to abiotic stress. J. Exp. Bot., 66(7):1749-1761.

[43]Zhang, B.H., Wang, Q.L., 2015. MicroRNA-based biotechnology for plant improvement. J. Cell. Physiol., 230(1):1-15.

[44]Zhang, B.H., Pan, X.P., Cobb, G.P., et al., 2006. Plant microRNA: a small regulatory molecule with big impact. Dev. Biol., 289(1):3-16.

[45]Zhang, B.H., Wang, Q.L., Pan, X.P., 2007. MicroRNAs and their regulatory roles in animals and plants. J. Cell. Physiol., 210(2):279-289.

[46]Zhong, R., Ye, Z.H., 2004. amphivasal vascular bundle 1, a gain-of-function mutation of the IFL1/REV gene, is associated with alterations in the polarity of leaves, stems and carpels. Plant Cell Physiol., 45(4):369-385.

[47]Zhu, H., Hu, F., Wang, R., et al., 2011. Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell, 145(2):242-256.

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