DNase I hypersensitive sites in two tissues of rice

Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice. Approximately 25% of the DH sites from both tissues were found in the putative promoters, indicating that the vast majority of gene regulatory elements in rice are not located at promoter regions. We found 58% more DH sites in callus than in seedling. For DH sites detected in both seedling and callus, 31% displayed significantly different levels of DNase I sensitivity within the two tissues. Genes that were differentially expressed in seedling and callus were frequently associated with DH sites in both tissues. The DNA sequences contained within the DH sites were hypomethylated, consistent with what is known about active gene regulatory elements. Interestingly, tissue-specific DH sites located in the promoters showed an elevated level of DNA methylation. A distinct elevation of H3K27me3 was associated with intergenic DH sites. These results suggest that epigenetic modifications play a role in the dynamic changes of the numbers and DNase I sensitivity of DH sites during development. For RNA-seq used in this project, please check GEO data GSE33265. Generation of genome-wide high resolution maps of DNase I hypersensitive sites in two tissues of rice. For seedling, we constructed 3 libraries (biological replicates) and sequenced a lane of Illumina Genome Analyzer for each library. For callus, we constructed 2 libraries (biological replicates). We sequenced two lanes for one library and one lane for another library.