title: Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays.
abstract: Epigenetic response to stress in plants involves changes in DNA methylation, histone modifications, and expression of small noncoding RNAs (sRNA). Here we present the method of analysis of differential expression of sRNA populations using DNA tiling arrays. sRNA extracted from Arabidopsis thaliana plants exposed to pathogen elicitor or control plants were reverse-transcribed into cDNAs, and subsequently hybridized after labeling 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 sRNA abundance.
authors: PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Ecole NormaleSupérieure, 46 rue d'Ulm, Paris, F75005, France. martine.boccara@upmc.fr.
authors: Martine
authors: M
authors: Boccara
authors: PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Ecole NormaleSupérieure, 46 rue d'Ulm, Paris, F75005, France.
authors: Alexis
authors: A
authors: Sarazin
authors: Atelier de bioinformatique, Sorbonne Universités, UMR 7205 (MNHN, UPMC, CNRS, EPHE), Museum national d'histoire naturelle, rueBuffon, Paris, F-7523, France.
authors: Bernard
authors: B
authors: Billoud
authors: PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Ecole NormaleSupérieure, 46 rue d'Ulm, Paris, F75005, France.
authors: Agnes
authors: A
authors: Bulski
authors: The Sainsbury Laboratory, John Innes Centre, Norwich, UK.
authors: Louise
authors: L
authors: Chapell
authors: The Sainsbury Laboratory, John Innes Centre, Norwich, UK.
authors: David
authors: D
authors: Baulcombe
authors: PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Ecole NormaleSupérieure, 46 rue d'Ulm, Paris, F75005, France.
authors: Vincent
authors: V
authors: Colot
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D058727:RNA, Small Untranslated / Q000235:genetics*; D015203:Reproducibility of Results; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D058727:RNA, Small Untranslated
keywords: Cy-dye indirect labeling; DNA tiling array; Harpin protein; Hypersensitive response; Microarray; Small RNA; cDNA libraries