Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome

Abstract

Transcriptional regulation is one of the most important processes for modulating gene expression. Though much of this control is attributed to transcription factors, histones, and associated enzymes, it is increasingly apparent that the spatial organization of chromosomes within the nucleus has a profound effect on transcriptional activity. Studies in yeast indicate that the nuclear pore complex might promote transcription by recruiting chromatin to the nuclear periphery. In higher eukaryotes, however, it is not known whether such regulation has global significance. Here we establish nucleoporins as a major class of global regulators for gene expression in Drosophila melanogaster. Using chromatin-immunoprecipitation combined with microarray hybridisation, we show that Nup153 and Megator (Mtor) bind to 25% of the genome in continuous domains extending 10 kb to 500 kb. These Nucleoporin-Associated Regions (NARs) are dominated by markers for active transcription, including high RNA polymerase II occupancy and histone H4K16 acetylation. RNAi–mediated knock-down of Nup153 alters the expression of ∼5,700 genes, with a pronounced down-regulatory effect within NARs. We find that nucleoporins play a central role in coordinating dosage compensation—an organism-wide process involving the doubling of expression of the male X chromosome. NARs are enriched on the male X chromosome and occupy 75% of this chromosome. Furthermore, Nup153-depletion abolishes the normal function of the male-specific dosage compensation complex. Finally, by extensive 3D imaging, we demonstrate that NARs contribute to gene expression control irrespective of their sub-nuclear localization. Therefore, we suggest that NAR–binding is used for chromosomal organization that enables gene expression control.

A role for DNA sequence in controlling the spatial organization of the genome

“…1C). [29][30][31] The interaction with these nucleoporins is required for proper expression of many of these genes. Therefore, movement of some genes to a specific nuclear landmark may not be required to interact with proteins that are concentrated at the NPC.…”

“…21,37,38 Artificially tethering of INO1 to the nuclear periphery enhances the rate of transcriptional activation 21 and tethering system, 28 which allow the visualization of a specific genetic locus with respect to nuclear landmarks. Genome-wide chromatin immunoprecipitation experiments with NPC proteins has defined a subset of the yeast 16,17 and fly genome [29][30][31] that interacts with the NPC and, in some cases is localized at the nuclear periphery (see below for exceptions). Among the genes that physically associate with the nuclear pore complex in yeast, we found an enrichment for genes with GRS I zip codes in their promoters.…”

Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila

“…The intranuclear accumulation of one such Nup, Nup98, is linked to ongoing nuclear transcription and chemical inhibition of RNA polymerase II was shown to abrogate its intranuclear mobility (17,18). Moreover, Nup98 was subsequently found to directly control gene expression of a subset of developmentally regulated genes (19)(20)(21). Nup98 is recruited to these loci during developmental transcriptional activation, and this association is required for the expression of such genes, particularly for the rapid induction of hormoneactivated developmental gene targets (19).…”

Linking dosage compensation and X chromosome nuclear organization inC. elegans

“…33 Fly DCC activates Xlinked gene transcription via H4K16 acetylation 34 and co-purifies with 2 nucleoporins, MTOR/TPR and NUP153. These nucleoporins interact broadly with the male X chromosome and are important for transcriptional upregulation and spatial positioning, 35,36 suggesting a functional link between dosage compensation and nuclear organization.…”