The present invention relates in one aspect to a method for analysing the frequency of interaction of a target nu-cleotide sequence with one or more nucleotide sequences of interest (eg. one or more genomic loci) comprising the steps of: (a) providing a sample of cross-linked DNA； (b) digesting the cross-linked DNA with a primary restriction enzyme； (c) ligating the cross-linked nucleotide sequences； (d) reversing the cross linking； (e) digesting the nucleotide sequences with a secondary restriction enzyme； (f) ligating one or more DNA sequences of known nucleotide composition to the available secondary restriction enzyme digestion site(s) that flank the one or more nucleotide sequences of interest； (g) amplifying the one or more nucleotide sequences of interest using at least two oligonucleotide primers, wherein each primer hybridises to the DNA sequences that flank the nucleotide sequences of interest； (h) hybridising the amplified sequence(s) to an array； and (i) determining the frequency of interaction between the DNA sequences.
