Drosophila MSL complex selectively identifies active genes on the male X chromosome

X-chromosome dosage compensation in Drosophila requires the male-specific lethal (MSL) complex, which up-regulates gene expression from the single male X chromosome. Here, we define X-chromosome-specific MSL binding at high resolution in two male cell lines and in late-stage embryos. We find that the MSL complex is highly enriched over most expressed genes, with binding biased toward the 3' end of transcription units. The binding patterns are largely similar in the distinct cell types, with ~600 genes clearly bound in all three cases. Genes identified as clearly bound in one cell type and not in another indicate that attraction of MSL complex correlates with expression state. Thus, sequence alone is not sufficient to explain MSL targeting. We propose that the MSL complex recognizes most X-linked genes, but only in the context of chromatin factors or modifications indicative of active transcription. Distinguishing expressed genes from the bulk of the genome is likely to be an important function common to many chromatin organizing and modifying activities. Keywords: ChIP-chip Comparison of MSL binding in two male cell lines (SL2 and Clone8) and in embryos: Tiling arrays containing 388,000 probes were designed based on FlyBase 3.2. Chromosome X and 19.6 Mb of chromosome 2L were tiled; chromosome 2L was useful as a control to verify that the features identified on the X are specific to it. For SL2 cells, two independent experiments were performed. Regions identified as bound in initial dye-swap replicates for the two SL2 experiments were very similar, and no further dye-swaps were performed. Two experiments and a dye-swap for one of them were used in the SL2 analysis. For Clone 8 cells and embryos, two experiments were performed for each cell type. Each experiment involved two arrays, one serving as a mock control in which the same protocol was followed in the absence of the TAP-tagged MSL complex. In total, seven log-ratio signals derived from 14 arrays were used: three for SL2 cells, two for Clone 8 cells, and two for embryos. The reproducibility between independent experiments within a cell type was excellent and care was taken to insure that the analysis is not biased by the uneven number of samples. In the embryo data, for instance, 776 and 766 clusters were identified in the two independent experiments and 757 were shared between the two.