Dosage compensation is the crucial process that equalizes gene expression from the X chromosome between males (XY) and females (XX). In Drosophila, the male-specific lethal (MSL) ribonucleoprotein complex mediates dosage compensation by upregulating transcription from the single male X chromosome approximately twofold. A key challenge is to understand how the MSL complex distinguishes the X chromosome from autosomes. Recent studies suggest that this occurs through a multi-step targeting mechanism that involves DNA sequence elements and epigenetic marks associated with transcription. This review will discuss the relative contributions of sequence elements and transcriptional marks to the complete pattern of MSL complex binding.

To facilitate the biochemical characterization of chromatin-associated proteins in the budding yeast Saccharomyces cerevisiae, we have developed a system to assemble nucleosomal arrays on immobilized templates using recombinant yeast core histones. This system enabled us to analyze the interaction of Isw2 ATPdependent chromatin remodeling complex with nucleosomal arrays. We found that Isw2 complex interacts efficiently with both naked DNA and nucleosomal arrays in an ATP-independent manner, suggesting that ATP is required at steps subsequent to this physical interaction. We identified the second subunit of Isw2 complex, encoded by open reading frame YGL 133w (herein named ITC1), and found that both subunits of the complex, Isw2p and Itc1p, are essential for efficient interaction with DNA and nucleosomal arrays. Both subunits are also required for nucleosome-stimulated ATPase activity and chromatin remodeling activity of the complex. Finally, we found that ITC1 is essential for function of Isw2 complex in vivo, since isw2 and itc1 deletion mutants exhibit virtually identical phenotypes. These results demonstrate the utility of our in vitro system in studying interactions between chromatin-associated proteins and nucleosomal arrays.The fundamental unit of chromatin is the nucleosome, composed of 147bp of DNA wrapped around an octamer of core histones H2A, H2B, H3, and H4 (29). Though required for genomic compaction, nucleosomes can inhibit processes dependent on protein-DNA interactions, including transcription. Therefore, chromatin remodeling is integral to the regulation of these processes. Two major classes of chromatin regulators have been identified in eukaryotic cells: histone-modifying enzymes and ATP-dependent chromatin remodeling factors (3,22,23,30,39,40,43,46,47,50,55). The significance of histone modifications in transcriptional regulation is highlighted by recent findings that a large number of previously identified transcriptional regulators possess acetylase and deacetylase activities (39,41,43). Acetylation of histone tails has been proposed to affect the higher-order folding of nucleosomal arrays (44) or the interaction of histone tails with DNA (54). Additionally, Strahl and Allis have proposed that histone modifications modulate the interactions of proteins with chromatin by serving as a code for recognition by specific proteins (39). However, the precise molecular mechanisms for the regulation of chromatin structure by covalent histone modifications remain to be determined.The second type of chromatin regulators, ATP-dependent chromatin remodeling factors, use the energy of ATP hydrolysis to alter chromatin structure. They have been grouped into three classes, SWI/SNF, ISWI, and CHD1, according to their ATPase subunits (7,20,22,32). Yeast SWI/SNF complex was originally identified as a positive regulator of a wide variety of genes (31, 53). Recent works suggest it may also have roles in the negative regulation of transcription (18,42). The founding member of the ISWI class, Drosophila ISWI, is e...

Drosophila MSL complex binds the single male X chromosome to upregulate gene expression to equal that from the two female X chromosomes. However, it has been puzzling that ~25% of transcribed genes on the X do not stably recruit MSL complex. Here, we find that almost all active genes on the X are associated with robust H4 Lys16 acetylation (H4K16ac), the histone modification catalyzed by MSL complex. The distribution of H4K16ac is much broader than that of MSL complex, and our results favor the idea that chromosome-wide H4K16ac reflects transient association of MSL complex, occurring through spreading or chromosomal looping. Our results parallel those of localized Polycomb repressive complex and its more broadly distributed H3K27me3 chromatin mark, suggesting a common principle for the establishment of active and silenced chromatin domains.