Analysis of chromatin condensation states by DNase I sensitivity assay at 500-base resolution in Arabidopsis

Variable levels of transgene expression are frequently observed among independent transgenic plants. Although different chromatin condensation states surrounding randomly integrated transgenes have previously been thought to be one of the causes for this variability, condensation states of plant chromatin have not been examined systematically. In this study, to analyze the condensation states of Arabidopsis chromatin, we evaluated the degree of chromatin condensation by measuring overall accessibility to DNase I (DNase I sensitivity) at 500-base resolution. We analyzed 30 variably expressed genes in an 80-kb genomic region, a gene repressed by polycomb group and heterochromatin protein 1-like genes, two genes near the heterochromatin, and a retrotransposon within the genetically-defined centromere in Arabidopsis. The centromeric region was significantly DNase I insensitive, however, sensitivity of these genes was similar irrespective of the individual gene expression levels.