Analysis of methylation status using nucleic acid arrays

Methods for amplifying a nucleic acid sample while preserving the methylation status of cytosines are disclosed. In some aspects the amplified methylated sample is modified by methylation sensitive modification and analyzed by hybridization to an array to identify cytosines that were methylated in the starting material and cytosines that were not methylated in the starting material. Methods for detecting methylation status are also disclosed. In one embodiment a DNA methyltransferase activity is included in the amplification reaction and this activity methylates the newly synthesized DNA using the methylated genomic template strand as a guide. Other aspects concern an array of probes which are complementary to restriction sites and methods for analysing methylation employing restriction enzymes and adaptors.