ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR240/095/SRR24064895/SRR24064895_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR240/096/SRR24064896/SRR24064896_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR240/099/SRR24064899/SRR24064899_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR240/099/SRR24064899/SRR24064899_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR240/098/SRR24064898/SRR24064898_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR240/096/SRR24064896/SRR24064896_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR240/097/SRR24064897/SRR24064897_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR240/097/SRR24064897/SRR24064897_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR240/098/SRR24064898/SRR24064898_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR240/095/SRR24064895/SRR24064895_2.fastq.gzprimary200OKGenomicsBecker, Molecular Biology, LMU Munichhttps://www.ebi.ac.uk/ena/browser/view/PRJNA952217Drosophila melanogasterxref:PubMed:37602401MSL2, the DNA-binding subunit of the Drosophila dosage compensation complex, cooperates with the ubiquitous protein CLAMP to bind MSL recognition elements (MREs) on the X chromosome. We explore the nature of the cooperative binding to these GA-rich, composite sequence elements in reconstituted naïve embryonic chromatin. We found that the cooperativity requires physical interaction between both proteins. Remarkably, disruption of this interaction does not lead to indirect, nucleosome-mediated cooperativity as expected, but to competition. The protein interaction apparently not only increases the affinity for composite binding sites, but also locks both proteins in a defined dimeric state that prevents competition. High Affinity Sites of MSL2 on the X chromosome contain variable numbers of MREs. We find that the cooperation between MSL2/CLAMP is not influenced by MRE clustering or arrangement, but happens largely at the level of individual MREs. The sites where MSL2/CLAMP bind strongly in vitro locate to all chromosomes and show little overlap to an expanded set of X-chromosomal MSL2 in vivo binding sites generated by CUT&RUN. Apparently, the intrinsic MSL2/CLAMP cooperativity is limited to a small selection of potential sites in vivo. This restriction must be due to components missing in our reconstitution, such as roX2 lncRNA. Overall design: Cut and Run profiles of MSL2 in S2 cell linesENACG1849, l(1)LB9, l(1)VE614, Runt, leg, Ct, DmelCG1849, Cell Lines, l(1)19Ea, Rnt, kf, CG11387, Cell, AA33, P235, lLB5, l(1)AA33, Cut, MSL2, MSL-2, DmelCG11387, l(1)B2/13.1, l(1)7Ba, RUN, Run, MSL2L1, l(1)7Bb, Line, CT, 1, 2, Cell., BcDNA:GH10590, MLS2, RNF184, LB5, LinesCG1849, l(1)LB9, l(1)VE614, Runt, leg, Ct, DmelCG1849, Cell Lines, l(1)19Ea, Rnt, kf, CG11387, Cell, AA33, P235, lLB5, l(1)AA33, Cut, MSL2, MSL-2, DmelCG11387, l(1)B2/13.1, l(1)7Ba, RUN, Run, MSL2L1, l(1)7Bb, Line, CT, 1, 2, Cell., BcDNA:GH10590, MLS2, RNF184, LB5, LinesfalseMSL2 cut and run profiles in S2 cell linesMSL2 cut and run profiles in S2 cell lines2025-09-242023-07-29PRJNA952217GSE228935722737602401