Sample and probe: a novel approach for identifying development-specific cis-elements of the enkephalin gene

We have developed a novel 'sample and probe' approach as a means to identifying specific DNA elements of the enkephalin gene that control differentiation of the enkephalinergic phenotype during neurodevelopment. The approach is a systematic spatiotemporal analysis of protein-DNA interactions; soluble nuclear proteins ('samples') prepared from microdissected regions of the developing brain are 'probed' with radiolabeled DNA fragments representing various regulatory regions of the enkephalin gene. The resulting spatiotemporal 'molecular maps', i.e. characteristic patterns of protein-DNA complexes showed DNA regions that harbor potential cis-elements regulating differentiation of the enkephalin phenotype at various stages of neurodevelopment. DNase I footprint analysis of such a DNA region identified a binding site (GACGGGAGATCGCTCGT) which is similar to the motif for a lymphoid-specific, developmentally regulated transcription factor, Ikaros, suggesting that the developing brain expresses Ikaros-like transcription factor(s) in a spatiotemporally defined manner. In summary, our approach offers a unique view into the chronology of coordinated protein-DNA interactions and will greatly facilitate identifying DNA elements and isolating development-specific transcription factors.