(A) MSL-mediated dosage compensation in Drosophila. The MSL complex consists of several proteins and noncoding RNAs (roX RNAs) and targets the X chromosome at CESs that contain the MSL-binding motif (as GA-rich sequence motif). (B) Formation of neo-sex chromosomes in Drosophila. The ancestral karyotype of Drosophila consists of five large rods (the ancestral X, which is conserved across Drosophila, and the autosomal arms Muller element B, C, D, and E) and the small dot chromosome (Muller element F). Autosomes repeatedly fused to the sex chromosomes, forming neo-X and neo-Y chromosomes. Loss of genes on the neo-Y creates selective pressure to dosage compensate neo-X genes and has repeatedly evolved in Drosophila by co-opting the MSL complex through the acquisition of novel MSL-binding sites. (C) ChIRP can be used to identify MSL-binding sites on Drosophila sex chromosomes. The roX RNA is bound in vivo to CESs; chromatin is cross-linked and fragmented, and roX2 is affinity purified and sequenced. CES, chromatin entry site; ChIRP, Chromatin Isolation by RNA Purification; MSL, male-specific lethal.