Reconstitution of MSL2 binding in vtiro

Transcription factors distinguish functional response elements from a large excess of similar sequences in metazoan genomes. Faithful discrimination relies on DNA sequence and shape, but how shape is modulated by chromatin organisation is unclear. We explored binding site selection principles by blending unique biological and experimental systems. First, we assemble Drosophila genomes into physiological embryonic chromatin as a substrate for genome-wide binding assays. Secondly, we monitor binding site selection of a protein, MSL2, for which all functional elements reside on the X chromosome. We observe direct and nucleosome-mediated cooperativity between MSL2 and two other transcription factors and discover an extended DNA shape signature of functional elements that is read out in chromatin. Strikingly, the physiological binding profile is not achieved through intrinsic properties of MSL2 but is sculpted by an unrelated transcription factor, GAF, that occludes non-functional sites. Our results reveal novel aspects of target selection in a complex chromatin environment. Chip-Seq profiles of Msl2 Clamp Gaf and Nurf on in vitro assembled chromatin. Mnase-seq Profiles of in vitro chromatin before and after addition of Clamp or H1.