Alekseyenko, A.A., Larschan, E., Lai, W.R., Park, P.J. & Kuroda, M.I. High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes Dev. 20, 848-857

Harvard University, Cambridge, Massachusetts, United States
Genes & Development (Impact Factor: 10.8). 05/2006; 20(7):848-57. DOI: 10.1101/gad.1400206
Source: PubMed


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 approximately 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.

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    • "Various figures have been reported for the number of genes that are expressed but not bound by MSL [11-14]. To determine how many of the compensated genes are significantly bound by the MSL-complex we used available MOF binding data from male salivary glands [28]. "
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    ABSTRACT: In organisms where the two sexes have unequal numbers of X-chromosomes, the expression of X-linked genes needs to be balanced not only between the two sexes, but also between X and the autosomes. In Drosophila melanogaster, the Male-Specific Lethal (MSL) complex is believed to produce a 2-fold increase in expression of genes on the male X, thus restoring this balance. Here we show that almost all the genes on the male X are effectively compensated. However, many genes are compensated without any significant recruitment of the MSL-complex. These genes are very weakly, if at all, affected by mutations or RNAi against MSL-complex components. In addition, even the genes that are strongly bound by MSL rely on mechanisms other than the MSL-complex for proper compensation. We find that long, non-ubiquitously expressed genes tend to rely less on the MSL-complex for their compensation and genes that in addition are far from High Affinity Sites tend to not bind the complex at all or very weakly. We conclude that most of the compensation of X-linked genes is produced by an MSL-independent mechanism. Similar to the case of the MSL-mediated compensation we do not yet know the mechanism behind the MSL-independent compensation that appears to act preferentially on long genes. Even if we observe similarities, it remains to be seen if the mechanism is related to the buffering that is observed in autosomal aneuploidies.
    Full-text · Article · Oct 2013 · Epigenetics & Chromatin
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    • "A previous RNA-seq study using D. melanogaster heads found a similar enrichment of X-linked sex-based genes and suggested that it was related the mechanism of dosage compensation that occurs on the male X chromosome [32]. To test for a possible influence of dosage compensation on sex-biased expression in the brain, we examined the correlation between the log2(male/female) expression ratio of all X-linked genes with at least 100 mapped reads in each sex and the distance to the nearest male-specific lethal (MSL) binding site [33], which represents the assembly point for the dosage compensation complex (DCC). The correlation was significantly negative (Spearman’s ρ = −0.11; "
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    ABSTRACT: Background Changes in gene regulation are thought to be crucial for the adaptation of organisms to their environment. Transcriptome analyses can be used to identify candidate genes for ecological adaptation, but can be complicated by variation in gene expression between tissues, sexes, or individuals. Here we use high-throughput RNA sequencing of a single Drosophila melanogaster tissue to detect brain-specific differences in gene expression between the sexes and between two populations, one from the ancestral species range in sub-Saharan Africa and one from the recently colonized species range in Europe. Results Relatively few genes (<100) displayed sexually dimorphic expression in the brain, but there was an enrichment of sex-biased genes, especially male-biased genes, on the X chromosome. Over 340 genes differed in brain expression between flies from the African and European populations, with the inter-population divergence being highly correlated between males and females. The differentially expressed genes included those involved in stress response, olfaction, and detoxification. Expression differences were associated with transposable element insertions at two genes implicated in insecticide resistance (Cyp6g1 and CHKov1). Conclusions Analysis of the brain transcriptome revealed many genes differing in expression between populations that were not detected in previous studies using whole flies. There was little evidence for sex-specific regulatory adaptation in the brain, as most expression differences between populations were observed in both males and females. The enrichment of genes with sexually dimorphic expression on the X chromosome is consistent with dosage compensation mechanisms affecting sex-biased expression in somatic tissues.
    Full-text · Article · Nov 2012 · BMC Genomics
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    • "Tandem affinity purification assay was performed as described in (Puig et al. 2001) with minor modifications: we used IgG agarose beads (Sigma) and acTEV protease (Invitrogen), Calmodulin binding step was omitted. Immunoprecipitation of MSL3-TAP fusion protein (Alekseyenko et al. 2006) was used as negative control. Immunoprecipitations with anti-PCNA antibodies were carried out using Protein A-sepharose beads (Sigma) according to the manufacturer's instructions. "
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    ABSTRACT: Drosophila SUUR (Suppressor of UnderReplication) protein was shown to regulate the DNA replication elongation process in endocycling cells. This protein is also known to be the component of silent chromatin in polyploid and diploid cells. To mark the different cell cycle stages, we used immunostaining patterns of PCNA, the main structural component of replication fork. We demonstrate that SUUR chromatin binding is dynamic throughout the endocyle in Drosophila salivary glands. We observed that SUUR chromosomal localization changed along with PCNA pattern and these proteins largely co-localized during the late S-phase in salivary glands. The hypothesized interaction between SUUR and PCNA was confirmed by co-immunoprecipitation from embryonic nuclear extracts. Our findings support the idea that the effect of SUUR on replication elongation depends on the cell cycle stage and can be mediated through its physical interaction with replication fork.
    Full-text · Article · Nov 2012 · Chromosoma
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