DNA Binding Signatures of the Myocyte Enhancer Factor-2B

DNA binding function of the myocyte enhancer factor-2B (MEF2B) is achieved through its unique capability of binding to target sites with a degenerate motif, while still functioning as a gene-specific transcriptional regulator. MEF2B-DNA recognition likely involves elements beyond the sequence of letters, aspects that are crucial to understand, particularly given recent evidence suggesting MEF2B regulatory role across a number of tissues and involvement with B-cell lymphoma. By coupling structural information, SELEX-seq and computational analysis, we were able to deduce sequence and shape determinants of MEF2B target sites at a high-throughput scale in vitro, based on which modeling binding affinities further exposed sequence-dependent shape patterns. The resulting binding signature of MEF2B reveals intricacies of DNA recognition mechanisms that, different from other TFs, sets it as a unique TF that combines base readout at the edges and shape readout at the center of its degenerate core-binding site. SELEX-seq was performed for the transcription factor MEF2B according to as described in Dantas et al. (to be submitted). Briefly, a DNA library 5’-GAGTTCTACAGTCCGACGATCCGC[N16]CCTGGAATTCTCGGGTGCCA-3’ , containing fixed sites and a random region of 16 base pairs (bp) (N16) was used in a binding reaction. Bound fragments were separated by electrophoretic mobility assay (EMSA), followed by isolation of DNA fragments and amplification by PCR. Two rounds of selection were performed. Final sequencing libraries were prepared using a 4-cycle PCR.