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.

Author Summary

The eukaryotic genome is spatially distributed in a highly organized manner, with chromosomal regions localizing to well-defined sub-nuclear positions. This organization could have a profound effect on chromatin accessibility and transcriptional activity on a genome-wide level. Using high-resolution, genome-wide, chromatin-binding profiles we show that the nuclear pore components Nup153 and Megator bind to quarter of the Drosophila genome in form of chromosomal domains. These domains represent active regions of the genome. Interestingly, comparison of male and female cells revealed enrichment of these domains on the male X chromosome, which represents an exceptionally active chromosome that is under dosage compensation control to equalize gene expression due to differences in X chromosome number between males and females. Based on extensive 3D image analysis, we show that these chromosomal domains are contributed by both peripheral as well as intranuclear pool of these proteins. We suggest that chromosomal organization by nucleoporins could contribute to global gene expression control.