The nucleus contains distinct nuclear bodies (NBs); nucleolus is the largest and the most studied NB, but its role in the functioning of the nucleus is far from being fully understood. The nucleolus is not surrounded by a membrane, yet it contains DNA, RNA and a set of proteins that can either be retained in the nucleolus or rapidly shuttle between the nucleoplasm, the nucleolus and the cytoplasm in response to various stimuli. The emerging evidence points to the central function of the nucleolus in organizing many nuclear functions besides RNA polymerase I transcription and ribosome biogenesis. Here we discuss the functions of the nucleolus related to the shuttling of proteins and nucleic acids between nucleolus and nucleoplasm. The functional processes affected by shuttling of nucleolar components include 3D organization of the genome, stress response, DNA repair and recombination, transcription regulation, telomere maintenance and other essential cellular functions. Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation Highlights  Nucleolus is a PolI transcription factory and a place of ribosome assembly, but is also performs many other functions that are commonly referred to as non-canonical functions of nucleolus  Nucleolus organizes the adjacent chromatin into a large-scale repressive hub underlying the spatial segregation of active and repressive chromatin compartments.  The interphase chromosomes are attached to the nucleolus via nucleolus-associated domains (NADs).  Protein shuttling between the nucleolus and the nucleoplasm regulates a multitude of nuclear processes including DNA repair, recombination, transcription and telomere maintenance.

The current progress in the study of the spatial organization of interphase chromosomes became possible owing to the development of the chromosome conformation capture (3C) protocol. The crucial step of this protocol is the proximity ligation—preferential ligation of DNA fragments assumed to be joined within nuclei by protein bridges and solubilized as a common complex after formaldehyde cross-linking and DNA cleavage. Here, we show that a substantial, and in some cases the major, part of DNA is not solubilized from cross-linked nuclei treated with restriction endonuclease(s) and sodium dodecyl sulphate and that this treatment neither causes lysis of the nucleus nor drastically affects its internal organization. Analysis of the ligation frequencies of the mouse β-globin gene domain DNA fragments demonstrated that the previously reported 3C signals were generated predominantly, if not exclusively, in the insoluble portion of the 3C material. The proximity ligation thus occurs within the cross-linked chromatin cage in non-lysed nuclei. The finding does not compromise the 3C protocol but allows the consideration of an active chromatin hub as a folded chromatin domain or a nuclear compartment rather than a rigid complex of regulatory elements.

It has been shown recently that apoptotic degradation of genomic DNA in mammalian cells starts by excision of large DNA fragments ranging in size from 50 kilobases to more than 300 kilobases. Although it was suggested that the above fragments could represent chromosomal DNA loops, the supposition was not supported by direct experimental evidence. In present work, we have studied the specificity of nucleolar and euchromatic gene long-range fragmentation in mouse and human cells triggered to undergo apoptosis either by tumor necrosis factor or by serum deprivation. Separation of the excised large DNA fragments by pulsed field gel electrophoresis followed by Southern analysis has demonstrated that in all cases studied the above fragmentation proceeds in a specific way. Furthermore, the patterns of DNA long-range fragmentation in the cells undergoing apoptosis were indistinguishable from the patterns of DNA cleavage into chromosomal loops by the high salt-insoluble topoisomerase II of the nuclear matrix. These results suggest the conclusion that apoptotic degradation of chromosomal DNA starts by excision of DNA loops and their oligomers.