The spatial organisation of DNA, both at the nucleotide and chromosomal levels, allows efficient storage of genetic information inside the nucleus. However, DNA-dependent processes such as transcription, require the chromosomal structure to be modified in order to allow access to this information.
The regulation of chromatin accessibility is an intensely studied subject 
. Molecular and genomic investigations have examined how nucleotide sequences and ATP-dependent chromatin-remodelling enzymes specify the locations for nucleosomal-binding, and how histone-modifying enzymes modulate the stability of histone-nucleic acid interactions. These enzymes are recruited to precise genomic loci with the aid of sequence-specific DNA-binding transcription factors. In turn, particular histone modifications influence transcription factor-binding to target sites on the genome, so controlling transcriptional initiation. Despite the importance of these cis- and trans-acting factors on the local chromosomal environment and the transcription of nearby genes, it has become increasingly clear that they explain just one level at which chromatin is regulated 
The eukaryotic genome is spatially distributed in a highly organised manner, with entire chromosomal regions localising to well-defined sub-nuclear positions 
. This organisation has a profound effect on chromatin accessibility and transcriptional activity on a genome-wide level 
. For instance, chromosomal regions at the nuclear envelope tend to form closed heterochromatin, a structure that is generally indicative of transcriptional repression 
. Genomic studies in Drosophila melanogaster
and humans established that lamins—proteins lining the nuclear membrane 
—are major contributors to sub-nuclear localisation and gene regulation 
. Comparisons of binding profiles with gene expression data and histone marker information showed that chromosomal regions containing dense lamin-binding were transcriptionally repressed.
Although the nuclear periphery has been primarily associated with repression, recent evidence has also suggested a role for membrane components in transcriptional activation 
. The nuclear pore complex is a large structure comprising about 30 protein subunits, and it is the primary channel through which macromolecules traverse the nuclear envelope 
. Interestingly, investigations in Saccharomyces cerevisiae
identified subunits of the nuclear pore complex that preferentially bound transcriptionally active genes 
. Moreover, several target loci such as GAL2 and INO1 were found to relocate from the interior to the periphery upon activation 
, although there were exceptions to this behaviour 
. Thus, it is becoming increasingly clear that nuclear periphery components can have both positive and negative influence on gene regulation.
Since there are differences in the composition of the nuclear envelope—such as the lack of lamins—it is important to also study the contribution of nuclear envelope components in gene regulation in higher organisms 
. So far just one study has explored the global interactions of nucleoporin subunit Nup93 with human chromosomes 5, 7 and 16 
; the publication reported only a low density of binding sites, and their influence on gene regulation was inconclusive.
Recently, we revealed a biochemical association between nucleoporins and the dosage compensation apparatus in higher eukaryotes including humans 
. In Drosophila
, the Male Specific Lethal (MSL) complex offsets the imbalance in the number of sex chromosomes in males and females by doubling the expression of genes on the male X chromosome 
. By purifying enzymatically active MOF complexes, we identified interactions with the nucleoporins Nup153 and Megator (Mtor). Strikingly, depletion of either subunit resulted in the loss of dosage compensation in male cells. Therefore, our work suggested a vital role for nucleoporins in promoting transcriptional activation on a large-scale.
Here, we present the first genome-wide study of nucleoporin-binding in a higher eukaryote. Using chromatin immunoprecipitation followed by hybridisation to high resolution tiling microarrays, we show that Nup153 and Mtor interact with 25% of the Drosophila genome in large domains spanning 10–500 kb in size. These regions—which we term nucleoporin associated regions (NARs)—contain large numbers of highly expressed genes, and are enriched for markers of active transcription including RNA polymerase-binding and histone H4 lysine 16 acetylation. Additionally, we reveal a remarkably high density of NARs on the male X chromosome, which correlate extremely well with the binding pattern of the dosage compensation complex. Finally, we demonstrate that chromosomal regions bound by these nucleoporins are composed of peripheral as well as non-peripheral pools of these proteins but interestingly the X chromosomal target regions are preferentially localised closer to the nuclear periphery. In summary, we firmly establish nucleoporins as a major class of chromatin-binding proteins in higher eukaryotes, with a general role in transcriptional regulation and three-dimensional chromosomal organisation. Finally we show for the first time, the importance of nucleoporin-binding not only as a mechanism for transcriptional control, but also in maintaining a complex organism-level biological system namely dosage compensation.