High-resolution ChIP–chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome
- Artyom A. Alekseyenko1,2,3,
- Erica Larschan2,3,
- Weil R. Lai2,
- Peter J. Park2,4,6, and
- Mitzi I. Kuroda1,2,3,5
- 1 Howard Hughes Medical Institute,
- 2 Harvard-Partners Center for Genetics and Genomics, Brigham and Women’s Hospital, Boston, Massachusetts 02115, USA;
- 3 Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
- 4 Children’s Hospital Informatics Program, Boston, Massachusetts 02115, USA
Abstract
X-chromosome dosage compensation in Drosophila requires the male-specific lethal (MSL) complex, which up-regulates gene expression from the single male X chromosome. Here, we define X-chromosome-specific MSL binding at high resolution in two male cell lines and in late-stage embryos. We find that the MSL complex is highly enriched over most expressed genes, with binding biased toward the 3′ end of transcription units. The binding patterns are largely similar in the distinct cell types, with ∼600 genes clearly bound in all three cases. Genes identified as clearly bound in one cell type and not in another indicate that attraction of MSL complex correlates with expression state. Thus, sequence alone is not sufficient to explain MSL targeting. We propose that the MSL complex recognizes most X-linked genes, but only in the context of chromatin factors or modifications indicative of active transcription. Distinguishing expressed genes from the bulk of the genome is likely to be an important function common to many chromatin organizing and modifying activities.
Keywords
Footnotes
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↵5 Corresponding authors.
↵5 E-MAIL mkuroda{at}genetics.med.harvard.edu; FAX (617) 525-4522.
- 6
↵6 E-MAIL peter_park{at}harvard.edu; FAX (617) 525-4488.
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Supplemental material is available at http://www.genesdev.org.
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Article published online ahead of print. Article and publication date are at http://www.genesdev.org/cgi/doi/10.1101/gad.1400206
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- Received December 12, 2005.
- Accepted February 3, 2006.
- Cold Spring Harbor Laboratory Press
