Analysis of small RNA populations using hybridization to DNA tiling arrays.
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.
Boccara
Martine
M
Unité de Recherche en Génomique Végétale, INRA/CNRS/UEVE, Evry cedex, France. martine.boccara@upmc.fr
Sarazin
Alexis
A
Billoud
Bernard
B
Bulski
Agnes
A
Chapell
Louise
L
Baulcombe
David
D
Colot
Vincent
V
D017360:Arabidopsis / Q000737:chemistry; D032461:Chromosomes, Plant / Q000235:genetics; D018076:DNA, Complementary; D018744:DNA, Plant; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D018749:RNA, Plant / Q000032:analysis*; D022661:RNA, Untranslated / Q000032:analysis*; D013312:Stress, Physiological / Q000235:genetics
D018076:DNA, Complementary; D018744:DNA, Plant; D018749:RNA, Plant; D022661:RNA, Untranslated