Identification of nucleosome depleted regions in Arabidopsis thaliana during oxidative stress

FAIRE is a procedure allowing the isolation of nucleosome-depleted regions from eukaryotic chromatin. With FAIRE different chromosomal regions are cross-linked to formaldehyde with different efficiencies, depending on the openness of the chromatin and their bound proteins. FAIRE has been employed to discover gene expression regulatory elements in a genome-wide scale. Such regions of the chromatin can be straightforwardly isolated using a simple biochemical phenol-chloroform extraction procedure after formaldehyde-mediated crosslinking of histones to chromosomal DNA and random fragmentation of the DNA by sonication. The extracted genomic DNA fragments are generally free of histones and represent regions containing regulatory elements, to which transcription factors could bind. Such genome segments can be further sequenced by next generation sequence technologies and thus identified. We established the FAIRE method for the analysis of regulatory elements in Arabidopsis. We used FAIRE on seedlings treated with 1mM 3-amino-1,2,4-triazole (3-AT) which inhibits catalase, thus leading to an intracellular rise in H2O2 level. FAIRE-isolated genomic fragments were subjected to deep sequencing resulting in around 100 million paired-end reads per sample (control and 3-AT-treated).