Chromatin immunoprecipitation of the MSL-1 and MSL-3 vs a mock IP in Drosophila and transcription profiling of X linked genes in WT male or female III instar larvae to provide X chromosome wide profiling of MSL-1 distribution and dosage compensation in Drosophila

Dosage compensation ensures that males and females, despite unequal number of X chromosomes, equalize for X linked gene expression. In Drosophila, it is achieved by a two-fold up-regulation of most of the genes present on the male X chromosome, and requires the association of the Dosage Compensation Complex (DCC) on the X chromosome. One of the main intriguing aspects of dosage compensation is how this complex is able to target specifically hundreds of sites only on the X chromosome in order to ensure dosage compensation. In order to better understand the targeting of the DCC and the dosage compensation mechanism, we have then decided to analyze the distribution of the DCC as well as the expression levels in male and female in a more complete and precise manner, using microarrays. In this experiment, we present the data used to analyse the distribution of the MSL-1 and MSL-3 protein (part of the DCC complex) on the X chromosome in WT embryos aged from 0H-14H, as well as the distribution of MSL-1 in embryos aged from 4-6H and in male III instar salivary glands. The DNA amplified from the specific immunoprecipitation (MSL-1 or MSL-3 IP) were labelled using Cy5-dCTP and hybridized against DNA amplified from a non specific immunoprecipitation (mock IP), labeled with Cy3 dye. In parralel we present the data used to analyse the expression profile of X-linked genes in WT male or female III instar larvae salivary glands. The cDNA amplified from the RNA extracted from the male or female salivary glands were labelled using Cy5-dUTP and hybridized against the reference sample, labelled with Cy3-dUTP (pool RNA from ON embryos, adultes, and salivary glands mixed at a ratio 1:1:1.and amplified as the RNA from salivary glands). We used for this study a cDNA array developed by the Genecore facility in EMBL, covering the DGC1 and DGC2 cDNA libraries from the Berkeley Drosophila Genome Project, which represents more than 70% of the coding Drosophila genome.