The present invention relates, e.g., to a method for isolating
a DNA molecule of interest in a form suitable for sequencing at least a portion of the
DNA by a high
throughput sequencing method, comprising (a) digesting a double-stranded (ds)
DNA molecule with two different restriction enzymes, A and B, to generate a ds form of the
DNA molecule of interest, which is bounded by the two
restriction enzyme cleavage products, and (b) attaching to each end of the DNA molecule of interest an adaptor molecule which comprises at one end a
restriction enzyme cleavage site that is compatible with the
restriction enzyme A or the restriction
enzyme B cleavage product, and which also comprises a sequence and / or element that allows the DNA of interest to be sequenced with a high
throughput sequencing apparatus. The method can be adapted for sequencing DNA with a variety of high
throughput sequencing apparatuses, including machines manufactured by the 454, Illumina (Solexa Sequencing technology) and ABI (
SOLiD™ Sequencing technology) companies. A method is also described for sequencing regulatory elements within a
cell, comprising subjecting a collection of ds DNA molecules that are enriched for regulatory elements and that are generated by
digestion with two restriction enzymes, A and B, which generate sticky ends, to an isolation method of the invention, and sequencing the collection of ds DNA molecules with a high throughput sequencing apparatus.