{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T09:47:18Z","timestamp":1782553638003,"version":"3.54.5"},"reference-count":108,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T00:00:00Z","timestamp":1782518400000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"German Research Council","award":["BE1140\/11-1"],"award-info":[{"award-number":["BE1140\/11-1"]}]},{"DOI":"10.13039\/100018173","name":"International Max-Planck Research School","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100018173","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Integrated Research Training Group"},{"name":"DFG-funded Collaborative Research Center"},{"name":"Ludwig-Maximilians-University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Metazoa evolved regulatory networks to balance sex chromosome expression. In Drosophila, males have a single gene-rich X chromosome, whereas females have two. Balanced X\/autosome expression is essential for viability, and in male flies is achieved by activation of genes on the X through the male-specific-lethal (MSL) dosage compensation complex (DCC). This ribonucleoprotein assembly contains long non-coding roX RNAs. To dissect the functional requirements of roX in a cell-based system, we deleted the roX2 gene in male S2 cells and selected two independent lines lacking detectable roX RNA. In the absence of roX, the remaining MSL protein complex was unable to associate with known or newly identified binding sites and thus failed to activate transcription. Surprisingly, the X\/autosome expression ratio appeared nevertheless compensated. Cytogenetic and genomic analyses revealed that both roX-deficient cell populations had acquired additional X chromosomes. We propose that uncompensated X expression compromises fitness and gives a selective growth advantage to cells that rebalance their genomes through chromosome mis-segregation. Remarkably, ectopic expression of roX2 reversed this selection, restored DCC binding, and normalized the karyotype. These findings illustrate that X chromosome dosage compensation is critical for viability even in cultured cells, and provide a striking example of rapid evolution under stringent selection.<\/jats:p>","DOI":"10.1093\/nar\/gkag649","type":"journal-article","created":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T12:23:36Z","timestamp":1781612616000},"source":"Crossref","is-referenced-by-count":0,"title":["Dosage compensation defects due to\n                    <i>roX<\/i>\n                    RNA loss are rescued by recalibration of X\/autosome stoichiometry"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-4859-4555","authenticated-orcid":false,"given":"Fotios","family":"Gkountromichos","sequence":"first","affiliation":[{"name":"Biomedical Center Munich, Molecular Biology Division, Ludwig-Maximilians-Universit\u00e4t , 82152 Planegg-Martinsried ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Yankson","sequence":"additional","affiliation":[{"name":"Department of Biology, Molecular Genetics, Technical University Darmstadt , Darmstadt 64289 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhunden","family":"Jayakrishnan","sequence":"additional","affiliation":[{"name":"Biomedical Center Munich, Molecular Biology Division, Ludwig-Maximilians-Universit\u00e4t , 82152 Planegg-Martinsried ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aline","family":"Campos\u00a0Sparr","sequence":"additional","affiliation":[{"name":"Biomedical Center Munich, Molecular Biology Division, Ludwig-Maximilians-Universit\u00e4t , 82152 Planegg-Martinsried ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5037-8154","authenticated-orcid":false,"given":"Marisa","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"Biomedical Center Munich, Molecular Biology Division, Ludwig-Maximilians-Universit\u00e4t , 82152 Planegg-Martinsried ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Heun","sequence":"additional","affiliation":[{"name":"Department of Biology, Molecular Genetics, Technical University Darmstadt , Darmstadt 64289 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7186-0372","authenticated-orcid":false,"given":"Peter B","family":"Becker","sequence":"additional","affiliation":[{"name":"Biomedical Center Munich, Molecular Biology Division, Ludwig-Maximilians-Universit\u00e4t , 82152 Planegg-Martinsried ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,27]]},"reference":[{"key":"2026062705302525600_B1","doi-asserted-by":"publisher","first-page":"a019398","DOI":"10.1101\/cshperspect.a019398","article-title":"Dosage compensation in Drosophila","volume":"7","author":"Lucchesi","year":"2015","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"2026062705302525600_B2","doi-asserted-by":"publisher","first-page":"3416","DOI":"10.3390\/cells10123416","article-title":"When down is up: heterochromatin, nuclear organization and X upregulation","volume":"10","author":"Makki","year":"2021","journal-title":"Cells"},{"key":"2026062705302525600_B3","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1534\/genetics.115.185108","article-title":"Dosage compensation in Drosophila\u2014a model for the coordinate regulation of transcription","volume":"204","author":"Kuroda","year":"2016","journal-title":"Genetics"},{"key":"2026062705302525600_B4","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1016\/S1097-2765(00)80193-8","article-title":"The roX1 and roX2 RNAs are essential components of the compensasome, which mediates dosage compensation in Drosophila","volume":"4","author":"Franke","year":"1999","journal-title":"Mol Cell"},{"key":"2026062705302525600_B5","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1016\/S0092-8674(00)81979-0","article-title":"Epigenetic spreading of the Drosophila dosage compensation complex from roX RNA genes into flanking chromatin","volume":"98","author":"Kelley","year":"1999","journal-title":"Cell"},{"key":"2026062705302525600_B6","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1016\/S0925-4773(03)00157-6","article-title":"Initiation of dosage compensation in Drosophila embryos depends on expression of the roX RNAs","volume":"120","author":"Meller","year":"2003","journal-title":"Mech Dev"},{"key":"2026062705302525600_B7","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1534\/genetics.106.064568","article-title":"roX RNAs are required for increased expression of X-linked genes in Drosophila melanogaster males","volume":"174","author":"Deng","year":"2006","journal-title":"Genetics"},{"key":"2026062705302525600_B8","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1016\/S0092-8674(00)81885-1","article-title":"roX1 RNA paints the X chromosome of male Drosophila and is regulated by the dosage compensation system","volume":"88","author":"Meller","year":"1997","journal-title":"Cell"},{"key":"2026062705302525600_B9","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1146\/annurev-genet-112414-055205","article-title":"Modulation of chromatin by noncoding RNA","volume":"49","author":"Meller","year":"2015","journal-title":"Annu Rev Genet"},{"key":"2026062705302525600_B10","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.1101\/gad.348411.121","article-title":"Divergent evolution toward sex chromosome-specific gene regulation in Drosophila","volume":"35","author":"Villa","year":"2021","journal-title":"Genes Dev"},{"key":"2026062705302525600_B11","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1101\/gad.272187.115","article-title":"Rapid evolutionary turnover underlies conserved lncRNA\u2013genome interactions","volume":"30","author":"Quinn","year":"2016","journal-title":"Genes Dev"},{"key":"2026062705302525600_B12","doi-asserted-by":"publisher","first-page":"e48138","DOI":"10.15252\/embr.201948138","article-title":"Progressive dosage compensation during Drosophila embryogenesis is reflected by gene arrangement","volume":"20","author":"Prayitno","year":"2019","journal-title":"EMBO Rep"},{"key":"2026062705302525600_B13","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1093\/emboj\/21.5.1084","article-title":"The roX genes encode redundant male-specific lethal transcripts required for targeting of the MSL complex","volume":"21","author":"Meller","year":"2002","journal-title":"EMBO J"},{"key":"2026062705302525600_B14","doi-asserted-by":"publisher","first-page":"e1007842","DOI":"10.1371\/journal.pgen.1007842","article-title":"RNA-on-X 1 and 2 in Drosophila melanogaster fulfill separate functions in dosage compensation","volume":"14","author":"Kim","year":"2018","journal-title":"PLoS Genet"},{"key":"2026062705302525600_B15","doi-asserted-by":"publisher","first-page":"1334","DOI":"10.1101\/gad.1082003","article-title":"Local spreading of MSL complexes from roX genes on the Drosophila X chromosome","volume":"17","author":"Oh","year":"2003","journal-title":"Genes Dev"},{"key":"2026062705302525600_B16","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1016\/0092-8674(91)90439-6","article-title":"The maleless protein associates with the X chromosome to regulate dosage compensation in Drosophila","volume":"66","author":"Kuroda","year":"1991","journal-title":"Cell"},{"key":"2026062705302525600_B17","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1016\/j.molcel.2013.07.001","article-title":"Tandem stem\u2013loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila","volume":"51","author":"Ilik","year":"2013","journal-title":"Mol Cell"},{"key":"2026062705302525600_B18","doi-asserted-by":"publisher","first-page":"1973","DOI":"10.1101\/gad.304600.117","article-title":"A mutually exclusive stem\u2013loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila","volume":"31","author":"Ilik","year":"2017","journal-title":"Genes Dev"},{"key":"2026062705302525600_B19","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/j.molcel.2013.06.011","article-title":"ATP-dependent roX RNA remodeling by the helicase maleless enables specific association of MSL proteins","volume":"51","author":"Maenner","year":"2013","journal-title":"Mol Cell"},{"key":"2026062705302525600_B20","first-page":"7483","article-title":"Two-step mechanism for selective incorporation of lncRNA into a chromatin modifier","volume":"48","author":"Muller","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2026062705302525600_B21","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1007\/s00412-005-0020-x","article-title":"Stable chromosomal association of MSL2 defines a dosage-compensated nuclear compartment","volume":"114","author":"Straub","year":"2005","journal-title":"Chromosoma"},{"key":"2026062705302525600_B22","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/s41586-020-2935-z","article-title":"RNA nucleation by MSL2 induces selective X chromosome compartmentalization","volume":"589","author":"Valsecchi","year":"2021","journal-title":"Nature"},{"key":"2026062705302525600_B23","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1007\/s00412-003-0249-1","article-title":"The MSL complex levels are critical for its correct targeting to the chromosomes in Drosophila melanogaster","volume":"112","author":"Demakova","year":"2003","journal-title":"Chromosoma"},{"key":"2026062705302525600_B24","doi-asserted-by":"publisher","first-page":"e5","DOI":"10.1371\/journal.pgen.0020005","article-title":"Targeting determinants of dosage compensation in Drosophila","volume":"2","author":"Dahlsveen","year":"2006","journal-title":"PLoS Genet"},{"key":"2026062705302525600_B25","doi-asserted-by":"publisher","first-page":"9039","DOI":"10.1093\/nar\/gkad680","article-title":"Physical interaction between MSL2 and CLAMP assures direct cooperativity and prevents competition at composite binding sites","volume":"51","author":"Eggers","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026062705302525600_B26","first-page":"391","article-title":"Drosphila cell lines as model systems and as an experimental tool","volume-title":"Methods Mol Biol","author":"Baum","year":"2008"},{"key":"2026062705302525600_B27","doi-asserted-by":"publisher","first-page":"2289","DOI":"10.1101\/gad.1343705","article-title":"Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster","volume":"19","author":"Hamada","year":"2005","journal-title":"Genes Dev"},{"key":"2026062705302525600_B28","doi-asserted-by":"publisher","first-page":"e1000320","DOI":"10.1371\/journal.pbio.1000320","article-title":"Expression in aneuploid Drosophila S2 cells","volume":"8","author":"Zhang","year":"2010","journal-title":"PLoS Biol"},{"key":"2026062705302525600_B29","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1101\/gr.146407.112","article-title":"Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq","volume":"23","author":"Straub","year":"2013","journal-title":"Genome Res"},{"key":"2026062705302525600_B30","doi-asserted-by":"publisher","first-page":"e56325","DOI":"10.7554\/eLife.56325","article-title":"Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms","volume":"9","author":"Scacchetti","year":"2020","journal-title":"eLife"},{"key":"2026062705302525600_B31","author":"Benchling"},{"key":"2026062705302525600_B32","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1038\/nbt.3437","article-title":"Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR\u2013Cas9","volume":"34","author":"Doench","year":"2016","journal-title":"Nat Biotechnol"},{"key":"2026062705302525600_B33","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1534\/genetics.113.160713","article-title":"Highly specific and efficient CRISPR\/Cas9-catalyzed homology-directed repair in Drosophila","volume":"196","author":"Gratz","year":"2014","journal-title":"Genetics"},{"key":"2026062705302525600_B34","doi-asserted-by":"crossref","article-title":"R: a language and environment for statistical computing","author":"R\u00a0Core\u00a0Team","DOI":"10.32614\/R.manuals"},{"key":"2026062705302525600_B35","doi-asserted-by":"publisher","first-page":"e46314","DOI":"10.7554\/eLife.46314","article-title":"Improved CUT&RUN chromatin profiling tools","volume":"8","author":"Meers","year":"2019","journal-title":"eLife"},{"key":"2026062705302525600_B36","doi-asserted-by":"publisher","first-page":"1706","DOI":"10.1093\/nar\/gky1238","article-title":"Factor cooperation for chromosome discrimination in Drosophila","volume":"47","author":"Albig","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026062705302525600_B37","doi-asserted-by":"publisher","first-page":"gkaf202","DOI":"10.1093\/nar\/gkaf202","article-title":"Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers","volume":"53","author":"Jayakrishnan","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026062705302525600_B38","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1016\/j.cell.2018.03.016","article-title":"Direct promoter repression by BCL11A controls the fetal to adult hemoglobin switch","volume":"173","author":"Liu","year":"2018","journal-title":"Cell"},{"key":"2026062705302525600_B39","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat Methods"},{"key":"2026062705302525600_B40","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1093\/bioinformatics\/btq046","article-title":"EBImage\u2014an R package for image processing with applications to cellular phenotypes","volume":"26","author":"Pau","year":"2010","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B41","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J Open Source Softw"},{"key":"2026062705302525600_B42","doi-asserted-by":"publisher","first-page":"861","DOI":"10.21105\/joss.00861","article-title":"UMAP: Uniform Manifold Approximation and Projection","volume":"3","author":"McInnes","year":"2018","journal-title":"J Open Source Softw"},{"key":"2026062705302525600_B43","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1109\/TSMC.1973.4309314","article-title":"Textural features for image classification","volume":"SMC-3","author":"Haralick","year":"1973","journal-title":"IEEE Trans Syst Man Cybern"},{"key":"2026062705302525600_B44","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/ncb2272","article-title":"Heterochromatin boundaries are hotspots for de novo kinetochore formation","volume":"13","author":"Olszak","year":"2011","journal-title":"Nat Cell Biol"},{"key":"2026062705302525600_B45","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2026062705302525600_B46","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B47","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B48","doi-asserted-by":"publisher","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ramirez","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026062705302525600_B49","doi-asserted-by":"publisher","first-page":"2204","DOI":"10.1093\/bioinformatics\/btq351","article-title":"BigWig and BigBed: enabling browsing of large distributed datasets","volume":"26","author":"Kent","year":"2010","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B50","doi-asserted-by":"publisher","first-page":"1008","DOI":"10.1093\/bioinformatics\/btt737","article-title":"WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis","volume":"30","author":"Zerbino","year":"2014","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B51","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsdottir","year":"2013","journal-title":"Briefings Bioinform"},{"key":"2026062705302525600_B52","doi-asserted-by":"publisher","first-page":"e45","DOI":"10.1093\/nar\/gkv1191","article-title":"csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows","volume":"44","author":"Lun","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026062705302525600_B53","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B54","doi-asserted-by":"publisher","first-page":"e1003118","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for computing and annotating genomic ranges","volume":"9","author":"Lawrence","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"2026062705302525600_B55","doi-asserted-by":"publisher","first-page":"2382","DOI":"10.1093\/bioinformatics\/btv145","article-title":"ChIPseeker: an R\/Bioconductor package for ChIP peak annotation, comparison and visualization","volume":"31","author":"Yu","year":"2015","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B56","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1038\/nature19338","article-title":"PionX sites mark the X chromosome for dosage compensation","volume":"537","author":"Villa","year":"2016","journal-title":"Nature"},{"key":"2026062705302525600_B57","doi-asserted-by":"publisher","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B58","doi-asserted-by":"publisher","first-page":"1841","DOI":"10.1093\/bioinformatics\/btp328","article-title":"rtracklayer: an R package for interfacing with genome browsers","volume":"25","author":"Lawrence","year":"2009","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B59","doi-asserted-by":"crossref","DOI":"10.32614\/R.manuals","article-title":"R: A language and environment for statistical computing","author":"R Core Team","year":"2025;"},{"key":"2026062705302525600_B60","doi-asserted-by":"publisher","first-page":"2834","DOI":"10.1093\/bioinformatics\/btab203","article-title":"STREME: accurate and versatile sequence motif discovery","volume":"37","author":"Bailey","year":"2021","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B61","doi-asserted-by":"publisher","first-page":"1603","DOI":"10.1093\/bioinformatics\/btr257","article-title":"Improved similarity scores for comparing motifs","volume":"27","author":"Tanaka","year":"2011","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B62","article-title":"Rsamtools: binary alignment (BAM), FASTA, variant call (BCF), and tabix file import","author":"Morgan","year":"2025"},{"key":"2026062705302525600_B63","doi-asserted-by":"publisher","first-page":"4757","DOI":"10.1093\/bioinformatics\/btz436","article-title":"snakePipes: facilitating flexible, scalable and integrative epigenomic analysis","volume":"35","author":"Bhardwaj","year":"2019","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B64","article-title":"FastQC: a quality control tool for high throughput sequence data","author":"Andrews","year":"2010"},{"key":"2026062705302525600_B65","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B66","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B67","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2026062705302525600_B68","article-title":"patchwork: the Composer of Plots","author":"Pedersen","year":"2025"},{"key":"2026062705302525600_B69","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1016\/j.molcel.2012.09.012","article-title":"MSL2 combines sensor and effector functions in homeostatic control of the Drosophila dosage compensation machinery","volume":"48","author":"Villa","year":"2012","journal-title":"Mol Cell"},{"key":"2026062705302525600_B70","doi-asserted-by":"publisher","first-page":"858","DOI":"10.1101\/gad.1399406","article-title":"Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex","volume":"20","author":"Gilfillan","year":"2006","journal-title":"Genes Dev"},{"key":"2026062705302525600_B71","doi-asserted-by":"publisher","first-page":"1252","DOI":"10.1128\/MCB.00910-07","article-title":"Incorporation of the noncoding roX RNAs alters the chromatin-binding specificity of the Drosophila MSL1\/MSL2 complex","volume":"28","author":"Li","year":"2008","journal-title":"Mol Cell Biol"},{"key":"2026062705302525600_B72","doi-asserted-by":"publisher","first-page":"e1004865","DOI":"10.1371\/journal.pgen.1004865","article-title":"Non-coding roX RNAs prevent the binding of the MSL-complex to heterochromatic regions","volume":"10","author":"Figueiredo","year":"2014","journal-title":"PLoS Genet"},{"key":"2026062705302525600_B73","doi-asserted-by":"publisher","first-page":"btaf375","DOI":"10.1093\/bioinformatics\/btaf375","article-title":"Benchmarking peak calling methods for CUT&RUN","volume":"41","author":"Nooranikhojasteh","year":"2025","journal-title":"Bioinformatics"},{"key":"2026062705302525600_B74","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1016\/j.cell.2008.06.033","article-title":"A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome","volume":"134","author":"Alekseyenko","year":"2008","journal-title":"Cell"},{"key":"2026062705302525600_B75","doi-asserted-by":"publisher","first-page":"e1000302","DOI":"10.1371\/journal.pgen.1000302","article-title":"The chromosomal high-affinity binding sites for the Drosophila dosage compensation complex","volume":"4","author":"Straub","year":"2008","journal-title":"PLoS Genet"},{"key":"2026062705302525600_B76","doi-asserted-by":"publisher","first-page":"7602","DOI":"10.1093\/nar\/gkab558","article-title":"Cell-free genomics reveal intrinsic, cooperative and competitive determinants of chromatin interactions","volume":"49","author":"Eggers","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026062705302525600_B77","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1186\/1471-2164-13-97","article-title":"Sequence signatures involved in targeting the male-specific lethal complex to X-chromosomal genes in Drosophila melanogaster","volume":"13","author":"Philip","year":"2012","journal-title":"BMC Genomics"},{"key":"2026062705302525600_B78","doi-asserted-by":"publisher","first-page":"5202","DOI":"10.1093\/emboj\/19.19.5202","article-title":"Targeting the chromatin-remodeling MSL complex of Drosophila to its sites of action on the X chromosome requires both acetyl transferase and ATPase activities","volume":"19","author":"Gu","year":"2000","journal-title":"EMBO J"},{"key":"2026062705302525600_B79","doi-asserted-by":"publisher","first-page":"6959","DOI":"10.1093\/nar\/gkv637","article-title":"Active promoters give rise to false positive \u2018Phantom Peaks\u2019 in ChIP-seq experiments","volume":"43","author":"Jain","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2026062705302525600_B80","doi-asserted-by":"publisher","first-page":"e09225","DOI":"10.7554\/eLife.09225","article-title":"A simple method for generating high-resolution maps of genome-wide protein binding","volume":"4","author":"Skene","year":"2015","journal-title":"eLife"},{"key":"2026062705302525600_B81","doi-asserted-by":"publisher","first-page":"e63274","DOI":"10.7554\/eLife.63274","article-title":"Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation","volume":"9","author":"Henikoff","year":"2020","journal-title":"eLife"},{"key":"2026062705302525600_B82","doi-asserted-by":"publisher","first-page":"eado5716","DOI":"10.1126\/sciadv.ado5716","article-title":"3D chromatin structures associated with ncRNA roX2 for hyperactivation and coactivation across the entire X chromosome","volume":"10","author":"Tian","year":"2024","journal-title":"Sci Adv"},{"key":"2026062705302525600_B83","doi-asserted-by":"publisher","first-page":"1551","DOI":"10.1101\/gad.214585.113","article-title":"The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation","volume":"27","author":"Soruco","year":"2013","journal-title":"Genes Dev"},{"key":"2026062705302525600_B84","doi-asserted-by":"publisher","first-page":"dev179663","DOI":"10.1242\/dev.179663r1","article-title":"The simultaneous interaction of MSL2 with CLAMP and DNA provides redundancy in the initiation of dosage compensation in Drosophila males","volume":"146","author":"Tikhonova","year":"2019","journal-title":"Development"},{"key":"2026062705302525600_B85","doi-asserted-by":"publisher","first-page":"3556","DOI":"10.1128\/MCB.01748-08","article-title":"Genome-wide mapping of Boundary Element-Associated Factor (BEAF) binding sites in Drosophila melanogaster links BEAF to transcription","volume":"29","author":"Jiang","year":"2009","journal-title":"Mol Cell Biol"},{"key":"2026062705302525600_B86","doi-asserted-by":"publisher","first-page":"37129","DOI":"10.1038\/s41598-025-21036-z","article-title":"Characterization of core promoter activation by the Drosophila insulator-binding protein BEAF","volume":"15","author":"Negedu","year":"2025","journal-title":"Sci Rep"},{"key":"2026062705302525600_B87","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.bbagrm.2007.11.011","article-title":"The DRE\/DREF transcriptional regulatory system: a master key for cell proliferation","volume":"1779","author":"Matsukage","year":"2008","journal-title":"Biochim Biophys Acta"},{"key":"2026062705302525600_B88","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1007\/s00412-016-0582-9","article-title":"Widespread colocalization of the Drosophila histone acetyltransferase homolog MYST5 with DREF and insulator proteins at active genes","volume":"126","author":"Heseding","year":"2017","journal-title":"Chromosoma"},{"key":"2026062705302525600_B89","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1016\/j.bbagrm.2017.03.004","article-title":"DREF plays multiple roles during Drosophila development","volume":"1860","author":"Tue","year":"2017","journal-title":"Biochim Biophys Acta"},{"key":"2026062705302525600_B90","doi-asserted-by":"publisher","first-page":"1509","DOI":"10.1093\/nar\/gkr869","article-title":"The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset","volume":"40","author":"Feller","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2026062705302525600_B91","doi-asserted-by":"publisher","first-page":"e1002736","DOI":"10.1371\/journal.pgen.1002736","article-title":"The NSL complex regulates housekeeping genes in Drosophila","volume":"8","author":"Lam","year":"2012","journal-title":"PLoS Genet"},{"key":"2026062705302525600_B92","doi-asserted-by":"publisher","first-page":"4889","DOI":"10.1093\/nar\/gkae123","article-title":"Processivity and specificity of histone acetylation by the male-specific lethal complex","volume":"52","author":"Kiss","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026062705302525600_B93","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1016\/j.molcel.2010.05.021","article-title":"The nonspecific lethal complex is a transcriptional regulator in Drosophila","volume":"38","author":"Raja","year":"2010","journal-title":"Mol Cell"},{"key":"2026062705302525600_B94","doi-asserted-by":"publisher","first-page":"1620","DOI":"10.1126\/science.1076686","article-title":"Extent of chromatin spreading determined by roX RNA recruitment of MSL proteins","volume":"298","author":"Park","year":"2002","journal-title":"Science"},{"key":"2026062705302525600_B95","doi-asserted-by":"publisher","DOI":"10.17912\/micropub.biology.001501","article-title":"Cell-type specific variation in X-chromosome dosage compensation in Drosophila","volume":"2025","author":"Pal","year":"2025","journal-title":"MicroPublBiol"},{"key":"2026062705302525600_B96","doi-asserted-by":"publisher","first-page":"R70","DOI":"10.1186\/gb-2014-15-8-r70","article-title":"DNA copy number evolution in Drosophila cell lines","volume":"15","author":"Lee","year":"2014","journal-title":"Genome Biol"},{"key":"2026062705302525600_B97","doi-asserted-by":"crossref","first-page":"R21","DOI":"10.1186\/gb-2012-13-3-r21","article-title":"The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome","volume":"13","author":"Cook","year":"2012","journal-title":"Genome Biol"},{"key":"2026062705302525600_B98","doi-asserted-by":"publisher","first-page":"e1006295","DOI":"10.1371\/journal.pgen.1006295","article-title":"Effects of gene dose, chromatin, and network topology on expression in Drosophila melanogaster","volume":"12","author":"Lee","year":"2016","journal-title":"PLoS Genet"},{"key":"2026062705302525600_B99","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1016\/j.devcel.2006.01.014","article-title":"Mislocalization of the Drosophila centromere-specific histone CID promotes formation of functional ectopic kinetochores","volume":"10","author":"Heun","year":"2006","journal-title":"Dev Cell"},{"key":"2026062705302525600_B100","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1038\/nrm2718","article-title":"Boveri revisited: chromosomal instability, aneuploidy and tumorigenesis","volume":"10","author":"Holland","year":"2009","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2026062705302525600_B101","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1038\/s41556-018-0243-8","article-title":"The diverse consequences of aneuploidy","volume":"21","author":"Chunduri","year":"2019","journal-title":"Nat Cell Biol"},{"key":"2026062705302525600_B102","doi-asserted-by":"publisher","first-page":"3859","DOI":"10.1242\/jcs.039537","article-title":"The consequences of tetraploidy and aneuploidy","volume":"121","author":"Storchova","year":"2008","journal-title":"J Cell Sci"},{"key":"2026062705302525600_B103","doi-asserted-by":"publisher","first-page":"1395","DOI":"10.1534\/genetics.115.185660","article-title":"Chromosome-specific and global effects of aneuploidy in Saccharomyces cerevisiae","volume":"202","author":"Dodgson","year":"2016","journal-title":"Genetics"},{"key":"2026062705302525600_B104","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1093\/gbe\/evp054","article-title":"Widespread transcriptional autosomal dosage compensation in Drosophila correlates with gene expression level","volume":"2","author":"McAnally","year":"2009","journal-title":"Genome Biol Evol"},{"key":"2026062705302525600_B105","doi-asserted-by":"publisher","first-page":"R28","DOI":"10.1186\/gb-2012-13-4-r28","article-title":"Mediation of Drosophila autosomal dosage effects and compensation by network interactions","volume":"13","author":"Malone","year":"2012","journal-title":"Genome Biol"},{"key":"2026062705302525600_B106","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/2042-6410-5-5","article-title":"Transcriptional effects of gene dose reduction","volume":"5","author":"Chen","year":"2014","journal-title":"Biol Sex Differ"},{"key":"2026062705302525600_B107","doi-asserted-by":"publisher","first-page":"2986","DOI":"10.1093\/nar\/gkx106","article-title":"Translational compensation of gene copy number alterations by aneuploidy in Drosophila melanogaster","volume":"45","author":"Zhang","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2026062705302525600_B108","doi-asserted-by":"publisher","first-page":"1700495","DOI":"10.1002\/biot.201700495","article-title":"Changes in chromosome counts and patterns in CHO cell lines upon generation of recombinant cell lines and subcloning","volume":"13","author":"Vcelar","year":"2018","journal-title":"Biotechnol J"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/12\/gkag649\/68631692\/gkag649.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/12\/gkag649\/68631692\/gkag649.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T09:30:37Z","timestamp":1782552637000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkag649\/8719431"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,22]]},"references-count":108,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2026,6,22]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkag649","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,7,8]]},"published":{"date-parts":[[2026,6,22]]},"article-number":"gkag649"}}