Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq

Genome Res. 2013 Mar;23(3):473-85. doi: 10.1101/gr.146407.112. Epub 2012 Dec 11.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Chromatin / genetics*
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation / methods*
  • DNA Fragmentation
  • DNA Helicases / genetics
  • DNA Helicases / metabolism
  • Dosage Compensation, Genetic*
  • Drosophila Proteins / genetics
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / genetics*
  • Drosophila melanogaster / metabolism
  • Genes, X-Linked
  • High-Throughput Nucleotide Sequencing
  • Histone Acetyltransferases / genetics
  • Histone Acetyltransferases / metabolism
  • Male
  • Multiprotein Complexes
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Promoter Regions, Genetic
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic
  • Transcriptional Activation
  • X Chromosome / genetics
  • X Chromosome / metabolism


  • Chromatin
  • Drosophila Proteins
  • Multiprotein Complexes
  • Nuclear Proteins
  • Transcription Factors
  • msl-1 protein, Drosophila
  • Histone Acetyltransferases
  • mof protein, Drosophila
  • DNA Helicases