title: Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq.
abstract: Transcriptional enhancement of X-linked genes to compensate for the sex chromosome monosomy in Drosophila males is brought about by a ribonucleoprotein assembly called Male-Specific-Lethal or Dosage Compensation Complex (MSL-DCC). This machinery is formed in male flies and specifically associates with active genes on the X chromosome. After assembly at dedicated high-affinity "entry" sites (HAS) on the X chromosome, the complex distributes to the nearby active chromatin. High-resolution, genome-wide mapping of the MSL-DCC subunits by chromatin immunoprecipitation (ChIP) on oligonucleotide tiling arrays suggests a rather homogenous spreading of the intact complex onto transcribed chromatin. Coupling ChIP to deep sequencing (ChIP-seq) promises to map the chromosomal interactions of the DCC with improved resolution. We present ChIP-seq binding profiles for all complex subunits, including the first description of the RNA helicase MLE binding pattern. Exploiting the preferential representation of direct chromatin contacts upon high-energy shearing, we report a surprising functional and topological separation of MSL protein contacts at three classes of chromosomal binding sites. Furthermore, precise determination of DNA fragment lengths by paired-end ChIP-seq allows decrypting of the local complex architecture. Primary contacts of MSL-2 and MLE define HAS for the DCC. In contrast, association of the DCC with actively transcribed gene bodies is mediated by MSL-3 binding to nucleosomes. We identify robust MSL-1/MOF binding at a fraction of active promoters genome-wide. Correlation analyses suggest that this association reflects a function outside dosage compensation. Our comprehensive analysis provides a new level of information on different interaction modes of a multiprotein complex at distinct regions within the genome.
authors.affiliation: Adolf-Butenandt-Institute and Center for Integrated Protein Science, Ludwig-Maximilians-University, D-80336 Munich, Germany. tobias.straub@lmu.de
authors.forename: Tobias
authors.initials: T
authors.lastname: Straub
authors.forename: Angelika
authors.initials: A
authors.lastname: Zabel
authors.forename: Gregor D
authors.initials: GD
authors.lastname: Gilfillan
authors.forename: Christian
authors.initials: C
authors.lastname: Feller
authors.forename: Peter B
authors.initials: PB
authors.lastname: Becker
mesh_terms: D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D053938:DNA Fragmentation; D004265:DNA Helicases / Q000235:genetics / Q000378:metabolism; D004303:Dosage Compensation, Genetic; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism; D050172:Genes, X-Linked; D059014:High-Throughput Nucleotide Sequencing; D051548:Histone Acetyltransferases / Q000235:genetics / Q000378:metabolism; D008297:Male; D046912:Multiprotein Complexes; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D015533:Transcriptional Activation; D014960:X Chromosome / Q000235:genetics / Q000378:metabolism
chemical_list: D002843:Chromatin; D029721:Drosophila Proteins; D046912:Multiprotein Complexes; D009687:Nuclear Proteins; D014157:Transcription Factors; C082132:msl-1 protein, Drosophila; D051548:Histone Acetyltransferases; C111063:mof protein, Drosophila; D004265:DNA Helicases