Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq
- 1 Ludwig Maximilians Univ.;
- 2 Adolf-Butenandt-Institute and Center for Integrated Protein Science, Ludwig-Maximilians-University,;
- 3 Norwegian Sequencing Centre, Department of Medical Genetics, Oslo University Hospital and Universit;
- 4 Adolf Butenandt Institut
- ↵* Corresponding author; email: pbecker{at}med.uni-muenchen.de
Abstract
Transcriptional enhancement of X-linked genes to compensate for the sex chromo-some monosomy in Drosophila males is brought about by a ribonucleoprotein assem-bly 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 the complex distributes to close-by active chromatin. High resolution, ge-nome-wide mapping of the MSL-DCC subunits by chromatin immunoprecipitation (ChIP) on oligonucleotide tiling arrays suggested a rather homogenous spreading of the intact complex onto transcribed chromatin. Coupling ChIP to deep sequencing (ChIP-seq) promises to map the chromosomal in-teractions of the DCC with improved resolution. We present ChIP-seq binding pro-files for all complex subunits including the first map of the RNA helicase MLE. Ex-ploiting 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 determi-nation of DNA fragment lengths by paired-end ChIP-seq allowed decrypting the local complex architecture. Primary contacts of MSL2 and MLE define HAS for the DCC. By contrast, association of the DCC with actively transcribed gene bodies is mediated by MSL3 binding to nucleosomes. We identify robust MSL1/MOF binding at a frac-tion of active promoters genome-wide. Correlation analyses suggest that this associa-tion reflects a function outside dosage compensation. Our comprehensive analysis provides a new level of information on different interac-tion modes of a multi-protein complex at distinct regions within the genome.
- Received July 20, 2012.
- Accepted December 10, 2012.
- © 2012, Published by Cold Spring Harbor Laboratory Press
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