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Plant Epigenetics pp 75–86Cite as

Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays

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Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 631))

Abstract

Small RNA (sRNA) populations extracted from Arabidopsis plants submitted or not to biotic stress, were reverse-transcribed into cDNAs, and these were subsequently hybridized after labelling to a custom-made DNA tiling array covering Arabidopsis chromosome 4. We first designed a control experiment with eight cDNA clones corresponding to sequences located on chromosome 4 and obtained robust and specific hybridization signals. Furthermore, hybridization signals along chromosome 4 were in good agreement with sRNA abundance as previously determined by Massive Parallel Sequence Signature (MPSS) in the case of untreated plants, but differed substantially after stress treatment. These results demonstrate the utility of hybridization to DNA tiling arrays to detect major changes in small RNA populations.

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Acknowledgments

MB was supported by a Visiting Scientist Fellowship from INRA. VC and DB are members of the European Union Network of Excellence “The Epigenome”.

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Authors and Affiliations

  1. Unité de Recherche en Génomique Végétale (URGV), INRA/CNRS/UEVE, Evry cedex, France

    Martine Boccara & Vincent Colot

  2. CNRS UMR8186, Département de biologie, Ecole Normale Supérieure, Paris cedex 05, France

    Alexis Sarazin

  3. Atelier de bioinformatique, Université Pierre et Marie Curie, Paris, France

    Bernard Billoud

  4. CNRS UMR8186, Département de biologie, Ecole Normale Supérieure, Paris cedex, France

    Agnes Bulski

  5. The Sainsbury Laboratory, John Innes Centre, Norwich, UK

    Louise Chapell & David Baulcombe

Authors
  1. Martine Boccara
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  2. Alexis Sarazin
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  3. Bernard Billoud
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  4. Agnes Bulski
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  5. Louise Chapell
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  6. David Baulcombe
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  7. Vincent Colot
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Corresponding author

Correspondence to Martine Boccara .

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Editors and Affiliations

  1. Dept. Biological Sciences, University of Lethbridge, University Drive 4401, Lethbridge, T1K 3M4, Canada

    Igor Kovalchuk

  2. Dept. Biological Sciences, University of Lethbridge, University Drive 4401, Lethbridge, T1K 3M4, Canada

    Franz J. Zemp

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Boccara, M. et al. (2010). Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays. In: Kovalchuk, I., Zemp, F. (eds) Plant Epigenetics. Methods in Molecular Biology™, vol 631. Humana Press. https://doi.org/10.1007/978-1-60761-646-7_8

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  • DOI: https://doi.org/10.1007/978-1-60761-646-7_8

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-645-0

  • Online ISBN: 978-1-60761-646-7

  • eBook Packages: Springer Protocols

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