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Chromatin immunoprecipitation on high-resolution tiling arrays and expression profiling were used to examine the binding of the male-specific lethal (MSL) complex to the Drosophila X chromosome. Shown here (background) is an immunofluoresence analysis of male polytene chromosomes using antibodies directed against TAP-tagged MSL3 (red), and DAPI-stained DNA (blue). Shown in the foreground is data representing the binding patterns derived from seven experiments on multiple cell types (SL2, red; Clone 8, green; embryo, blue). A large number of genes bound by the MSL complex were identified and differential binding patterns in different cell types revealed a correlation between binding and expression state. (For details, see Alekseyenko et al., p. 848, and related papers by Gilfillan et al., p. 858, and Legube et al., p. 871. The authors would like to thank Dr. Sek Won Kong for help with the cover illustration.)