Mechanistic Basis for Chromosomal Translocations at the E2A Gene and its Broader Relevance to Human B Cell Malignancies

Bisulfite chemical probing of DNA structure under native (nondenaturing) conditions is an ideal high-resolution method to assess stable or transient single-stranded states. Cytosine conversion in the native bisulfite assay is a measure of transient single-stranded character in double stranded DNA (dsDNA). Sequence-specific primers were used to amplify the non-transcribed strand and transcribed strand of the region around the E2A fragile zone in its intron 16 from native ammonium bisulfite treated Nalm-6 and 697 pre-B cells. Traditional bisulfite sequencing measures the methylated cytosines. The non-transcribed strand of the region around the E2A fragile zone was amplified by fully converted primers from Nalm-6, Reh, and 697 genomic DNA after sodium bisulfite treatment at denatured condition.