Dosage compensation of sex chromosomes in Drosophila melanogaster is an excellent model system to study various aspects of targeting of protein factors to chromatin. Dosage compensation prevents male lethality by up regulating transcription from the single male X chromosome in the ~2 fold range to match the two active X chromosomes in females [reviewed in e.g. (Ferrari et al., 2014; Kuroda et al., 2016; Samata and Akhtar, 2018)]. This up regulation is facilitated by the male specific lethal

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... ) dosage compensation complex (DCC). The DCC binds selectively to ~300 high affinity sites (HAS) on the X chromosome, containing a low complexity GAGA rich sequence motif, the MSL recognition element (MRE) (Alekseyenko et al., 2008; Straub et al., 2008). However, the DCC neglects thousands of other similar sequences in the genome outside of HAS. The DNA binding subunit MSL2 alone can enrich X chromosomal MREs in vitro, although MSL2 misses most MREs within HAS (Villa et al., 2016). The Chromatin Linked Adaptor for MSL Proteins (CLAMP) binds thousands of MREs genome wide and contributes to DCC targeting to HAS (Kaye et al., 2018; Soruco et al., 2013). The role of CLAMP in facilitating MSL2 targeting to HAS was investigated by several approaches. Monitoring MSL2 chromatin binding in vivo by chromatin immunoprecipitation with high throughput sequencing (ChIP seq) showed the requirement of CLAMP for HAS targeting. Next, the interplay between CLAMP and MSL2 in genome wide in vitro DNA binding was studied by DNA immunoprecipitation with high throughput sequencing (DIP seq) (Gossett and Lieb, 2008; Liu et al., 2005; Villa et al., 2016). The data revealed mutual recruitment of both factors to each other's binding sites and cooperative binding to novel sites. This DNA binding cooperativity extended each other's binding repertoire to facilitate robust binding of MREs located within HAS, although increased binding to other non functional sites was observed. Both factors interacted directly with each other in co IP experiments, provid [...]