Regional Control of Chromatin Organization by Noncoding roX RNAs and the NURF Remodeling Complex in Drosophila melanogaster

X Bai,S Y Kwon,M I Kuroda,P Badenhorst,E Larschan

doi:10.1534/genetics.107.071571

X Bai, S Y Kwon + Show 3 more

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https://doi.org/10.1534/genetics.107.071571

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Abstract

Dosage compensation in Drosophila is mediated by a histone-modifying complex that upregulates transcription of genes on the single male X chromosome. The male-specific lethal (MSL) complex contains at least five proteins and two noncoding roX (RNA on X) RNAs. The mechanism by which the MSL complex targets the X chromosome is not understood. Here we use a sensitized system to examine the function of roX genes on the X chromosome. In mutants that lack the NURF nucleosome remodeling complex, the male polytene X chromosome is severely distorted, appearing decondensed. This aberrant morphology is dependent on the MSL complex. Strikingly, roX mutations suppress the Nurf mutant phenotype regionally on the male X chromosome. Furthermore, a roX transgene induces disruption of local flanking autosomal chromatin in Nurf mutants. Taken together, these results demonstrate the potent capability of roX genes to organize large chromatin domains in cis, on the X chromosome. In addition to interacting functions at the level of chromosome morphology, we also find that NURF complex and MSL proteins have opposing effects on roX RNA transcription. Together, these results demonstrate the importance of a local balance between modifying activities that promote and antagonize chromatin compaction within defined chromatin domains in higher organisms.

Highlights

THE compaction of eukaryotic DNA into nucleosomes and higher-order chromatin structure has profound effects on gene transcription
We find that the aberrant morphology of the male X chromosome in Nurf301 mutants can be regionally suppressed by deletion of either roX1 or roX2, providing strong evidence that roX genes function over very long distances along the X chromosome
The roX noncoding RNAs are critical components that regulate targeting of male-specific lethal (MSL) complexes to the male X chromosome. roX RNAs are not stably expressed in wild-type females, and here we show that nucleosome remodeling factor (NURF), an ATPdependent chromatin-remodeling enzyme, is a repressor of roX transcription in females

Summary

Introduction

THE compaction of eukaryotic DNA into nucleosomes and higher-order chromatin structure has profound effects on gene transcription. Our previous studies suggest that nascent roX RNA transcripts serve as local nucleation sites for assembly of the complex (Park et al 2002; Bai et al 2004). This can be seen when roX transgenes are inserted at ectopic positions on the autosomes, when the endogenous X chromosome lacks both roX genes. NURF is the founding member of the imitation switch (ISWI) family of ATP-dependent chromatin-remodeling factors These are multisubunit protein complexes that use the energy of ATP hydrolysis to slide nucleosomes. Reconstitution experiments reveal that only NURF301 and ISWI are essential for the chromatin-remodeling activities of NURF, suggesting that they are the major subunits (Xiao et al 2001)

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