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. 2006 Apr 1;20(7):871-83.
doi: 10.1101/gad.377506. Epub 2006 Mar 17.

X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila

Gaëlle Legube  1 , Shannon K McWeeney, Martin J Lercher, Asifa Akhtar
Affiliations

X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila

Gaëlle Legube et al. Genes Dev. .

Abstract

In Drosophila, dosage compensation is achieved by a twofold up-regulation of the male X-linked genes and requires the association of the male-specific lethal complex (MSL) on the X chromosome. How the MSL complex is targeted to X-linked genes and whether its recruitment at a local level is necessary and sufficient to ensure dosage compensation remain poorly understood. Here we report the MSL-1-binding profile along the male X chromosome in embryos and male salivary glands isolated from third instar larvae using chromatin immunoprecipitation (ChIP) coupled with DNA microarray (ChIP-chip). This analysis has revealed that majority of the MSL-1 targets are primarily expressed during early embryogenesis and many target genes possess DNA replication element factor (DREF)-binding sites in their promoters. In addition, we show that MSL-1 distribution remains stable across development and that binding of MSL-1 on X-chromosomal genes does not correlate with transcription in male salivary glands. These results show that transcription per se on the X chromosome cannot be the sole signal for MSL-1 recruitment. Furthermore, genome-wide analysis of the dosage-compensated status of X-linked genes in male and female shows that most of the X chromosome remains compensated without direct MSL-1 binding near the gene. Our results, therefore, provide a comprehensive overview of MSL-1 binding and dosage-compensated status of X-linked genes and suggest a more global effect of MSL complex on X-chromosome regulation.

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Figures

Figure 1.
Figure 1.
Binding of MSL-1 and MSL-3 in 0–14-h Drosophila embryos. (A) Chromosomal distribution of MSL-1 target genes in 0–14-h embryos, defined as the genes showing a rank percentile > 95%, and a p-value < 0.1. The majority of these genes are located on the X chromosome as shown. (B) Distribution of MSL-1 (in red) and MSL-3 (in green) on three cytological bands of the X chromosome. Each vertical line represents the average MSL-1/MOCK ratio of a probed gene at its chromosomal position (in megabases). Positions of the DGC clones spotted on the array are presented below each graph. The roX1 gene is indicated by an arrow. Asterisk indicates cluster of genes represented in C. (C) Detailed view of a cluster of genes located in the 14 cytological band.
Figure 2.
Figure 2.
MSL-1 binds on active genes early in development. Clustered expression profiles of target and nontarget genes of MSL-1 in 0–14-h embryos. Most target genes are predominantly expressed in embryos. Red indicates high expression level, green indicates low expression level. Gene expression data were taken from Arbeitman et al. (2002).
Figure 3.
Figure 3.
Similar distribution of MSL-1 binding between 4–6-h embryos and salivary glands of third instar larvae. (A) Distribution of MSL-1 in 4–6-h-staged embryos (in red) and in male third instar larvae salivary glands (in blue) on the same three cytological bands of the X chromosome represented in Figure 1B. (B) Bivariate scatterplot of MSL-1/MOCK log ratio in 4–6-h embryos and in third instar larvae salivary glands of all probed loci on the X chromosome.
Figure 4.
Figure 4.
MSL-1 binding correlates poorly with transcription in male salivary glands. (A) Bivariate scatterplots of MSL-1/MOCK ChIP data and time point/pool expression data. MSL-1/MOCK log ratio is obtained from the 4–6-h ChIP–chip data set (left panel) and from the male third instar salivary glands ChIP–chip data set (middle and right panels). Time point/pool log ratio are obtained from the 4–5-h (in black) and 5–6-h (in blue) time points (left panel); from the 96-h (in blue) and 105-h (in black) time points (middle panel) (Arbeitman et al. 2002); and from the male salivary gland expression data set (analyzed from four independent experiments, our results) (right panel). (B) Immunofluorescence analysis of the distribution of MSL-1 and of three transcription-associated factors on male polytene chromosomes from third instar larvae Spt5, Spt6, and RNA polymerase II (PolII-S5-P; phosphorylated on the Ser 5 of the CTD).
Figure 5.
Figure 5.
Direct MSL-1 binding is uncoupled at a local level with dosage compensation. (A) Bivariate scatter plot of the expression data (expressed as log ratio) obtained from male and female salivary glands, for the clones located on the X chromosome. (B, top) qPCR analysis of the RNA level in third instar salivary glands, in male and female, of nine genes “targeted” by MSL-1 according to our ChIP–chip analysis in larvae (p < 0.1, rank percentile > 95%), and seven genes defined as “not targeted” in salivary glands (p > 0.6, rank percentile < 60%). The genes that were part of the dosage-compensated subset according to the expression array data are shown in blue (FDR p = 1), whereas the genes in red showed an adjusted FDR p-value < 0.1; i.e., female-biased expression. All RNA levels were normalized against GAPDH. Male RNA levels are expressed as percentage of female expression level set at 100%. (Bottom) Binding profile of MSL-1 on the corresponding genes in the top panel represented by fold enrichment of MSL-1/MOCK in ChIP–chip salivary glands data set.
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References

    1. Aggarwal B.D., Calvi B.R. Chromatin regulates origin activity in Drosophila follicle cells. Nature. 2004;430:372–376. - PubMed
    1. Akhtar A., Becker P.B. Activation of transcription through histone H4 acetylation by MOF, an acetyl transferase essential for dosage compensation in Drosophila. Mol. Cell. 2000;5:367–375. - PubMed
    1. Arbeitman M.N., Furlong E.E., Imam F., Johnson E., Null B.H., Baker B.S., Krasnow M.A., Scott M.P., Davis R.W., White K.P. Gene expression during the life cycle of Drosophila melanogaster. Science. 2002;297:2270–2275. - PubMed
    1. Baker B.S., Gorman M., Marin I. Dosage compensation in Drosophila. Annu. Rev. Genet. 1994;28:491–521. - PubMed
    1. Belyakin S.N., Christophides G.K., Alekseyenko A.A., Kriventseva E.V., Belyaeva E.S., Nanayev R.A., Makunin I.V., Kafatos F.C., Zhimulev I.F. Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories. Proc. Natl. Acad. Sci. 2005;102:8269–8274. - PMC - PubMed

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