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Non Coding RNAs in Plants pp 79–89Cite as

Genome-Wide Analysis of RNA Degradation in Arabidopsis

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Part of the book series: RNA Technologies ((RNATECHN))

Abstract

During the past 10 years, a number of new findings have been made in RNA-mediated gene regulation and in regulation mechanisms of the RNAs using some advanced high-throughput technologies in the model plant, Arabidopsis thaliana. One of them is a genome-wide tiling array that allows us to receive the information of strand-specific transcriptome of not only protein-coding mRNAs but also long non coding transcripts. This chapter introduces several findings on plant nonsense-mediated decay (NMD), a well-known RNA regulatory machinery, and also summarizes the results of genome-wide analyses of RNA regulatory networks through NMD and NMD-related decay pathways, some of which have already been examined using the microarrays such as the tiling array. Their analyses revealed that unnecessary RNA species including long non coding junk RNAs are downregulated by the RNA decay machineries such as NMD. This chapter will help understand the existence of the transcriptional hidden layer and how genome-wide transcriptome is being constructed in plants.

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Acknowledgments

This work was supported by a grant from RIKEN Plant Science Center (to M.S.) and by Grants-in-Aid for Scientific Research on Kiban (C) (no. 21570056) and on Priority Areas (no. 21027033) of the Ministry of Education, Culture, Sports, Science, and Technology of Japan (to M.S.). Y.K. was supported by a JSPS Postdoctoral Fellowship for Research Abroad.

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Authors and Affiliations

  1. Plant Genomic Network Research Team, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama-shi, 230-0045, Japan

    Motoaki Seki

  2. Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, 244-0813, Japan

    Motoaki Seki

  3. Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA

    Yukio Kurihara

Authors
  1. Yukio Kurihara
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  2. Motoaki Seki
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Correspondence to Motoaki Seki .

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Editors and Affiliations

  1. Institute of Chemistry/Biochemistry, Free University Berlin, Thielallee 63, Berlin, 14195, Berlin, Germany

    Volker A. Erdmann

  2. Inst. Bioorganic Chemistry, PAN Poznan, ul. Z. Noskowskiego 12/14, Poznan, 61-704, Poland

    Jan Barciszewski

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Kurihara, Y., Seki, M. (2011). Genome-Wide Analysis of RNA Degradation in Arabidopsis . In: Erdmann, V., Barciszewski, J. (eds) Non Coding RNAs in Plants. RNA Technologies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19454-2_6

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