The nuclear lamina binds chromatin in vitro and is thought to function in its organization, but genes that interact with it are unknown. Using an in vivo approach, we identified approximately 500 Drosophila melanogaster genes that interact with B-type lamin (Lam). These genes are transcriptionally silent and late replicating, lack active histone marks and are widely spaced. These factors collectively predict lamin binding behavior, indicating that the nuclear lamina integrates variant and invariant chromatin features. Consistently, proximity of genomic regions to the nuclear lamina is partly conserved between cell types, and induction of gene expression or active histone marks reduces Lam binding. Lam target genes cluster in the genome, and these clusters are coordinately expressed during development. This genome-wide analysis gives clear insight into the nature and dynamic behavior of the genome at the nuclear lamina, and implies that intergenic DNA functions in the global organization of chromatin in the nucleus.

Nuclear pore complexes (NPCs) mediate transport across the nuclear envelope. In yeast, they also interact with active genes, attracting or retaining them at the nuclear periphery. In higher eukaryotes, some NPC components (nucleoporins) are also found in the nucleoplasm, with a so far unknown function. We have functionally characterized nucleoporin-chromatin interactions specifically at the NPC or within the nucleoplasm in Drosophila. We analyzed genomic interactions of full-length nucleoporins Nup98, Nup50, and Nup62 and nucleoplasmic and NPC-tethered forms of Nup98. We found that nucleoporins predominantly interacted with transcriptionally active genes inside the nucleoplasm, in particular those involved in developmental regulation and the cell cycle. A smaller set of nonactive genes interacted with the NPC. Genes strongly interacting with nucleoplasmic Nup98 were downregulated upon Nup98 depletion and activated on nucleoplasmic Nup98 overexpression. Thus, nucleoporins stimulate developmental and cell-cycle gene expression away from the NPC by interacting with these genes inside the nucleoplasm.

Nuclear pore complexes (NPCs) are multiprotein complexes consisting of nucleoporins and function in transport between the nucleus and the cytoplasm. In yeast, nucleoporins have also been linked to gene expression as well as to chromatin insulating activity. Recently, we identified genomic regions that interact with nucleoporins in Drosophila using DamID technology. We found that nucleoporins in the nucleoplasm interact with active genes and stimulate gene expression. However, genes interacting with nucleoporins at the NPC itself show average gene expression and it remains unclear why they interact with the NPC. Here, we further investigated the function of the genome-NPC interactions. First, to investigate whether a different technique would lead to similar results, we compared our nucleoporin DamID data to recently published nucleoporin chromatin immunoprecipitation (ChIP) data. Then, to further understand the function of interactions between the genome and NPCs, we analyzed the relationship between NPC-interacting genomic regions and chromatin insulators. We found that the insulator protein Su(Hw) was enriched within and near NPC-interacting genomic regions, suggesting a role of this protein in chromatin architecture close to the NPC. This suggests that the NPC may have a function in the structural organization of the genome.

In the limited space of the nucleus, chromatin is organized in a dynamic and non-random manner. Three ways of chromatin organization are compaction, formation of loops and localization within the nucleus. To study chromatin localization it is most convenient to use the nuclear envelope as a fixed viewpoint. Peripheral chromatin has both been described as silent chromatin, interacting with the nuclear lamina, and active chromatin, interacting with nuclear pore proteins. Current data indicate that the nuclear envelope is a reader as well as a writer of chromatin state, and that its influence is not limited to the nuclear periphery. Ó 2008 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.Keywords: Chromatin; Nuclear lamina; Lamin; Nuclear pore complex; Nucleoporin; Nup Chromatin organization by compactionTo fit into the limited space of the nucleus and still carry out its function, human genomic DNA is extensively folded, making it about 10 000-fold more compact. Several levels of compaction have been described: the nucleosome, the 30 nm fiber and higher order chromatin structure.The lowest level of chromatin compaction is the nucleosome. A 5-10-fold compaction is achieved when 146-165 base pairs of DNA are wound around an octamer of histone proteins, which is referred to as the nucleosome core particle. Besides providing a structural basis for the first compaction level, histones can also affect chromatin organization by being chemically modified at their tail or by being replaced by variants of the core histones. These modifications have a major impact on chromatin structure and gene expression by influencing the binding of proteins to the nucleosome, the affinity of DNA for the histone octamer and the stability of higher order structures [1]. Thus, at this low level of organization the nucleosome offers a powerful mechanism for controlling chromatin structure in a local, non-random manner.Findings on the second level of compaction are more ambiguous. In vitro, oligonucleosomes are able to organize themselves into a compact fiber with a diameter of 30 nm in absence of nuclear proteins but in the presence of divalent cations. In vivo, estimated nuclear cation concentrations are even higher than the concentration used in experiments, aiding the compaction [2]. This compaction could be further modulated by the involvement of numerous nuclear proteins in vivo. For example, histone tails and histone H1 further stabilize this structure by binding to linker DNA.All condensation levels above the 30 nm fiber are indicated as higher order chromatin structure. This poorly defined structure may consist of several levels of condensation and is very dynamic and thus hard to study. The question has even been raised whether there is a uniform higher order structure at all, or whether chromatin is too dynamic to form stable structures at a higher order level [3].All levels of compaction are not equal throughout the cell, leading to more accessible and less accessible regions. D...