Development and application of a method to study DNA methylation and chromatin structure at the chromosome domain level

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In order to develop a method to study DNA methylation and chromtin structure of large genomic regions, we combined the methylation-sensitive restriction assay and nuclease-sensitivity assay with field-inversion gel electrophoresis (FIGE). The distal region of mouse chromosome 7, which comprises the imprinted ins2/lgf2/H19 genes, was analyzed in model expeniments. When 100 kb of the region was scanned by this method for DNasel hypersensitive sites, three new clusters of hypersensitive sites were identified. It was possible to study fragments larger than 25 kb. Similarly, it was possible to determine the methylation status of genomic regions larger than 25 kb after partial digestion with HpaII and HhaI.The reliability of these methods was comfirmed by examining the same regions by the conventional, short-range methods. We also found that partial degestion with HpaII and HhaI was useful for identifying and mapping CpG islands in native genomic and cloned DNA.The usefulness of the method has been shown with lambda, cosmid and P1 clones containing various inserts and a fragment as large as 85 kb could be analyzed at once. These methods are quite simple and reliable and thus can be applied to the long-range analysis of genome and chromatin structure.