A Transgenic Transcription Factor (TaDREB3) in Barley Affects the Expression of MicroRNAs and Other Small Non-coding RNAs

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2012 Aug 8

PMID 22870277

Citations 20

Authors

Michael Hackenberg

Bu-Jun Shi

Perry Gustafson

Peter Langridge

Affiliations

Soon will be listed here.

Abstract

Transcription factors (TFs), microRNAs (miRNAs), small interfering RNAs (siRNAs) and other functional non-coding small RNAs (sRNAs) are important gene regulators. Comparison of sRNA expression profiles between transgenic barley over-expressing a drought tolerant TF (TaDREB3) and non-transgenic control barley revealed many group-specific sRNAs. In addition, 42% of the shared sRNAs were differentially expressed between the two groups (|log(2)| >1). Furthermore, TaDREB3-derived sRNAs were only detected in transgenic barley despite the existence of homologous genes in non-transgenic barley. These results demonstrate that the TF strongly affects the expression of sRNAs and siRNAs could in turn affect the TF stability. The TF also affects size distribution and abundance of sRNAs including miRNAs. About half of the sRNAs in each group were derived from chloroplast. A sRNA derived from tRNA-His(GUG) encoded by the chloroplast genome is the most abundant sRNA, accounting for 42.2% of the total sRNAs in transgenic barley and 28.9% in non-transgenic barley. This sRNA, which targets a gene (TC245676) involved in biological processes, was only present in barley leaves but not roots. 124 and 136 miRNAs were detected in transgenic and non-transgenic barley, respectively. miR156 was the most abundant miRNA and up-regulated in transgenic barley, while miR168 was the most abundant miRNA and up-regulated in non-transgenic barley. Eight out of 20 predicted novel miRNAs were differentially expressed between the two groups. All the predicted novel miRNA targets were validated using a degradome library. Our data provide an insight into the effect of TF on the expression of sRNAs in barley.

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References

Li W, Oono Y, Zhu J, He X, Wu J, Iida K . The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell. 2008; 20(8):2238-51. PMC: 2553615. DOI: 10.1105/tpc.108.059444. View

Hsieh T, Lee J, Yang P, Charng Y, Wang Y, Chan M . Heterology expression of the Arabidopsis C-repeat/dehydration response element binding factor 1 gene confers elevated tolerance to chilling and oxidative stresses in transgenic tomato. Plant Physiol. 2002; 129(3):1086-94. PMC: 166503. DOI: 10.1104/pp.003442. View

Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F . Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell. 2008; 133(1):116-27. PMC: 2981139. DOI: 10.1016/j.cell.2008.02.034. View

Jurka J, Kapitonov V, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J . Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005; 110(1-4):462-7. DOI: 10.1159/000084979. View

Oh S, Kim Y, Kwon C, Park H, Jeong J, Kim J . Overexpression of the transcription factor AP37 in rice improves grain yield under drought conditions. Plant Physiol. 2009; 150(3):1368-79. PMC: 2705040. DOI: 10.1104/pp.109.137554. View

Saski C, Lee S, Fjellheim S, Guda C, Jansen R, Luo H . Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Theor Appl Genet. 2007; 115(4):571-90. PMC: 2674615. DOI: 10.1007/s00122-007-0567-4. View

Morin R, Aksay G, Dolgosheina E, Ebhardt H, Magrini V, Mardis E . Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res. 2008; 18(4):571-84. PMC: 2279245. DOI: 10.1101/gr.6897308. View

Masotti A, Caputo V, Da Sacco L, Pizzuti A, Dallapiccola B, Bottazzo G . Quantification of small non-coding RNAs allows an accurate comparison of miRNA expression profiles. J Biomed Biotechnol. 2009; 2009:659028. PMC: 2735750. DOI: 10.1155/2009/659028. View

Buhler M, Spies N, Bartel D, Moazed D . TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat Struct Mol Biol. 2008; 15(10):1015-23. PMC: 3240669. DOI: 10.1038/nsmb.1481. View

10.

Siomi M, Sato K, Pezic D, Aravin A . PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol. 2011; 12(4):246-58. DOI: 10.1038/nrm3089. View

11.

Pederson T . Regulatory RNAs derived from transfer RNA?. RNA. 2010; 16(10):1865-9. PMC: 2941095. DOI: 10.1261/rna.2266510. View

12.

Rajagopalan R, Vaucheret H, Trejo J, Bartel D . A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 2006; 20(24):3407-25. PMC: 1698448. DOI: 10.1101/gad.1476406. View

13.

Wang J, Czech B, Weigel D . miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell. 2009; 138(4):738-49. DOI: 10.1016/j.cell.2009.06.014. View

14.

Wu G, Park M, Conway S, Wang J, Weigel D, Poethig R . The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell. 2009; 138(4):750-9. PMC: 2732587. DOI: 10.1016/j.cell.2009.06.031. View

15.

Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas Jr A, Zhu J . A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci U S A. 2006; 103(47):18002-7. PMC: 1693862. DOI: 10.1073/pnas.0608258103. View

16.

Babiarz J, Ruby J, Wang Y, Bartel D, Blelloch R . Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev. 2008; 22(20):2773-85. PMC: 2569885. DOI: 10.1101/gad.1705308. View

17.

Agarwal P, Agarwal P, Reddy M, Sopory S . Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep. 2006; 25(12):1263-74. DOI: 10.1007/s00299-006-0204-8. View

18.

Borsani O, Zhu J, Verslues P, Sunkar R, Zhu J . Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell. 2005; 123(7):1279-91. PMC: 3137516. DOI: 10.1016/j.cell.2005.11.035. View

19.

Ouyang S, Buell C . The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res. 2003; 32(Database issue):D360-3. PMC: 308833. DOI: 10.1093/nar/gkh099. View

20.

Lu C, Tej S, Luo S, Haudenschild C, Meyers B, Green P . Elucidation of the small RNA component of the transcriptome. Science. 2005; 309(5740):1567-9. DOI: 10.1126/science.1114112. View