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Genome-Wide Identification, Biochemical Characterization, and Expression Analyses of the YTH Domain-Containing RNA-Binding Protein Family in Arabidopsis and Rice

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Abstract

RNA-binding proteins are critical to RNA metabolism in cells and, thus, play important roles in diverse biological processes. In the present study, we identified the YTH domain-containing RNA-binding protein (RBP) family in Arabidopsis thaliana and rice at the molecular and biochemical levels. A total of 13 and 12 genes were found to encode YTH domain-containing RBPs in Arabidopsis and rice and named as AtYTH01–13 and OsYTH01–12, respectively. The phylogeny, chromosomal location, and structures of genes and proteins were analyzed. Electrophoretic mobility shift assays demonstrated that recombinant AtYTH05 protein could bind to single-stranded RNA in vitro, demonstrating that the YTH proteins have RNA-binding activity. Analyses of publicly available microarray data, gene expression by qRT-PCR, and AtYTH05 promoter activity indicate that the Arabidopsis AtYTHs and rice OsYTHs genes have distinct and diverse expression patterns in different tissues and developmental stages, showing tissue- and developmental-specific expression patterns. Furthermore, analyses of publicly available microarray data also indicate that many of the Arabidopsis AtYTHs and rice OsYTHs genes might be involved in responses to various abiotic and biotic stresses as well as in response to hormones. Our data demonstrate that the YTH family proteins are a novel group of RBPs and provide useful clues to define their biological functions of this RBP family in plants.

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Acknowledgments

This work was supported by the National Key Project for Research on Transgenic Plants (2011ZX08009-003-001), the National Natural Science Foundation of China (Nos. 31101422 and 31272028), the National High-Tech R&D Program (No. 2012AA101504), and the Research Fund for the Doctoral Program of Higher Education of China (20120101110070).

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The authors declare that they have no conflict of interest.

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  1. State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China

    Dayong Li, Huijuan Zhang, Yongbo Hong, Lei Huang, Xiaohui Li, Yafen Zhang, Zhigang Ouyang & Fengming Song

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  1. Dayong Li
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  2. Huijuan Zhang
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  3. Yongbo Hong
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Correspondence to Fengming Song.

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Li, D., Zhang, H., Hong, Y. et al. Genome-Wide Identification, Biochemical Characterization, and Expression Analyses of the YTH Domain-Containing RNA-Binding Protein Family in Arabidopsis and Rice. Plant Mol Biol Rep 32, 1169–1186 (2014). https://doi.org/10.1007/s11105-014-0724-2

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