In previous reports, SELEX-seq profiling followed by DNA shape analyses of binding by heterodimers of all eight Drosophila melanogaster Hox proteins in complex with their common co-factor Extradenticle (Exd) revealed an important role for MGW readout [26, cuatro9]. More recently, an extension of the SELEX-seq method for methylated binding sites, EpiSELEX-seq, revealed that cytosine methylation modulates the affinity with which human orthologs (Pbx-Hox) of these heterodimers bind to CpG dinucleotide-containing sites . The DNA sequences associated with the largest binding affinity for the Exd-Hox and Pbx-Hox complexes matched the 12-bp sequence pattern NTGAYNNAYNNN, where Y represents pyrimidine (C or T) and N any nucleotide (Fig.
Eg, methylation off an excellent CpG dinucleotide during the counterbalance six/seven (NTGA greatY
