With the vast transcriptome database now available, global patterns of gene expression have been mapped in various species to reveal higher order structures in the genome. Location-dependent control of gene expression has also been studied in human cell cultures and in Arabidopsis plants using well-characterized insertion and transposition cell line collections. With the added genome-wide mapping of chromatin features at a high resolution, via advanced microarray and sequencing technologies, comprehensive analysis of structure–function relationships deduced from chromatin organization and gene expression data is now feasible. This has begun to reveal micro-heterogeneity in the genome with respect to structural and functional segmentations.