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

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.T HE compaction of eukaryotic DNA into nucleosomes and higher-order chromatin structure has profound effects on gene transcription. By modifying nucleosome structure or altering nucleosome positioning, histone-modifying enzymes and ATP-dependent chromatin-remodeling factors modulate chromatin architecture and thereby regulate gene expression. A major question is how the disparate activities of these chromatinorganizing enzymes are deployed and integrated.

Incorporation of the Noncoding roX RNAs Alters the Chromatin-Binding Specificity of the Drosophila MSL1/MSL2 Complex

“…The results shown in Fig. 5C and D were obtained with the roX1 and roX2 primer pairs used by Bai et al (4); however, similar results were obtained with different roX1 and roX2 primer pairs (data not shown). Further, comparable results were obtained with independently isolated RNA preparations (not shown).…”

Dosage Compensation inDrosophila

“…In contrast, the absence of either roX gene reduces the abnormal puffing of the X in the region of the roX mutation. This observation highlights the localized nature of opposing activities that are responsible for normal chromatin organization (Bai et al 2007). …”

“…Mutants in nurf301 show the abnormally decondensed male X seen in Iswi mutants (Badenhorst et al 2002). NURF also has a specific effect on roX1 and roX2 transcription; wild-type NURF negatively regulates these genes in females and reduces the level of transcription of roX2 in males by approximately one half (Bai et al 2007). …”

Haploinsufficiency of the Chromatin Remodeler BPTF Causes Syndromic Developmental and Speech Delay, Postnatal Microcephaly, and Dysmorphic Features

“…To date, neither INO80/SWR1 nor ISWI genes have been associated with disease in humans. The ISWI family member NURF (nucleosome remodeling factor) is an evolutionarily conserved key transcriptional regulator of development 2 in a locus-specific manner 3,4 by virtue of the complex's chromatin remodeling activity. 5,6 In vertebrates, NURF consists of SNF2L (ISWI homolog encoded by SMARCA1), pRBAP46/48, and the largest subunit BPTF (bromodomain PHD finger transcription factor).…”