SUV39h‐ and A‐type lamin‐dependent telomere nuclear rearrangement

Telomeres are specialized chromatin structures that are situated at the end of linear chromosomes and play an important role in cell senescence and immortalization. Here, we investigated whether changes in histone signature influence the nuclear arrangement and positioning of telomeres. Analysis of mouse embryonic fibroblasts revealed that telomeres were organized into specific clusters that partially associated with centromeric clusters. This nuclear arrangement was influenced by deficiency of the histone methyltransferase SUV39h, LMNA deficiency, and the histone deacetylase inhibitor Trichostatin A (TSA). Similarly, nuclear radial distributions of telomeric clusters were preferentially influenced by TSA, which caused relocation of telomeres closer to the nuclear center. Telomeres also co‐localized with promyelocytic leukemia bodies (PML). This association was increased by SUV39h deficiency and decreased by LMNA deficiency. These differences could be explained by differing levels of the telomerase subunit, TERT, in SUV39h‐ and LMNA‐deficient fibroblasts. Taken together, our data show that SUV39h and A‐type lamins likely play a key role in telomere maintenance and telomere nuclear architecture. J. Cell. Biochem. 109: 915–926, 2010. © 2010 Wiley‐Liss, Inc.     

Nuclear matrix binding site in the Rad51 recombinase

It has been shown that the key homologous recombination protein Rad51accumulates in DNA damage‐induced nuclear foci that are attached to the nuclear matrix. In the present communication we attempted to find whether Rad51 contains a functional domain responsible for nuclear matrix binding. By alignments of the sequences encoding nuclear matrix targeting signals of human nuclear matrix binding proteins with the whole length human Rad51sequence a putative nuclear matrix targeting signal was identified. To prove that it is responsible for the nuclear matrix association of Rad51 18 base pairs encoding a cluster of hydrophobic amino acids in the human Rad51 Flag‐tagged gene were deleted. The formation of damage‐induced Rad51 foci and their association with the nuclear matrix were monitored in HeLa cells transfected with the wild‐type and the mutated Rad51gene after treatment with mitomycin C. The results showed that while the wild‐type protein formed Rad51 foci attached to the nuclear matrix, the mutated Rad51 failed to form DNA damage‐induced nuclear foci. The loss of foci formation activity of the mutated protein was not due to impaired ability to bind double‐stranded DNA in an ATP‐dependant way in vitro and to bind chromatin in vivo. These data suggest that the assembly of Rad51 into nuclear foci is assisted by association with the nuclear matrix, which may support the spatial organization of the process of repair by homologous recombination. J. Cell. Physiol. 219: 202–208, 2009. © 2008 Wiley‐Liss, Inc.     

Mobility of Nuclear Components and Genome Functioning

Cell nucleus is characterized by strong compartmentalization of structural components in its three-dimensional space. Certain genomic functions are accompanied by changes in the localization of chromatin loci and nuclear bodies. Here we review recent data on the mobility of nuclear components and the role of this mobility in genome functioning.     

A new nuclear protease with cathepsin L properties is present in HeLa and Caco‐2 cells

Recently many authors have reported that cathepsin L can be found in the nucleus of mammalian cells with important functions in cell‐cycle progression. In previous research, we have demonstrated that a cysteine protease (SpH‐protease) participates in male chromatin remodeling and in cell‐cycle progression in sea urchins embryos. The gene that encodes this protease was cloned. It presents a high identity sequence with cathepsin L family. The active form associated to chromatin has a molecular weight of 60 kDa, which is higher than the active form of cathepsin L described until now, which range between 25 and 35 kDa. Another difference is that the zymogen present in sea urchin has a molecular weight of 75 and 90 kDa whereas for human procathepsin L has a molecular weight of 38–42 kDa. Based on these results and using a polyclonal antibody available in our laboratory that recognizes the active form of the 60 kDa nuclear cysteine protease of sea urchin, ortholog to human cathepsin L, we investigated the presence of this enzyme in HeLa and Caco‐2 cells. We have identified a new nuclear protease, type cathepsin L, with a molecular size of 60 kDa, whose cathepsin activity increases after a partial purification by FPLC and degrade in vitro histone H1. This protease associates to the mitotic spindle during mitosis, remains in the nuclei in binuclear cells and also translocates to the cytoplasm in non‐proliferative cells. J. Cell. Biochem. 111: 1099–1106, 2010. © 2010 Wiley‐Liss, Inc.     

Comparison of replicative and non-replicative chromatin assembly pathways in HeLa cell extracts.

It has been reported that chromatin assembly in mammalian cell extracts depends exclusively or preferentially on ongoing DNA replication (Stillman, B. (1986) Cell 45, 555-565). More recently, this view has been challenged demonstrating that, in the same extracts, chromatin can also be formed efficiently in the absence of DNA replication (Gruss et al. (1990) EMBO J. 9, 2911-2922). The experiments, described in this communication, were performed to resolve this apparent contradiction. We found that there are at least two distinct in vitro pathways for chromatin assembly in HeLa cell extracts. The replicative pathway requires a nuclear protein, most likely identical with the chromatin assembly factor, described by Stillman (1986, Cell 45, 555-565), and the free soluble histones present in the cytosol of S phase cells. In contrast, a non-replicative pathway was identified that depends on isolated nuclear histones. As one component of the non-replicative assembly pathway we identified a cytosolic factor that was purified to apparent homogeneity and shown to be an acidic 50 kDa polypeptide. The isolated cytosolic 50 kDa protein efficiently promoted nucleosome assembly as demonstrated by one- and two-dimensional gel electrophoresis of in vitro packaged plasmid DNA.     

Chromatin binding of the fission yeast replication factor mcm4 occurs during anaphase and requires ORC and cdc18

We describe an in situ technique for studying the chromatin binding of proteins in the fission yeast Schizosaccharomyces pombe. After tagging the protein of interest with green fluorescent protein (GFP), chromatin-associated protein is detected by GFP fluorescence following cell permeabilization and washing with a non-ionic detergent. Cell morphology and nuclear structure are preserved in this procedure, allowing structures such as the mitotic spindle to be detected by indirect immunofluorescence. Cell cycle changes in the chromatin association of proteins can therefore be determined from individual cells in asynchronous cultures. We have applied this method to the DNA replication factor mcm4/cdc21, and find that chromatin association occurs during anaphase B, significantly earlier than is the case in budding yeast. Binding of mcm4 to chromatin requires orc1 and cdc18 (homologous to Cdc6 in budding yeast). Release of mcm4 from chromatin occurs during S phase and requires DNA replication. Upon overexpressing cdc18, we show that mcm4 is required for re-replication of the genome in the absence of mitosis and is associated with chromatin in cells undergoing re-replication.     

ChIP‐based methods for the identification of long‐range chromatin interactions

Chromatin immunoprecipitation (ChIP) is an important technique for studying protein–DNA interactions. Whole genome ChIP methods have enjoyed much success, but are limited in that they cannot uncover important long‐range chromatin interactions. Chromosome conformation capture (3C) and related methods are capable of detecting remote chromatin interactions, but are tedious, have low signal‐to‐noise ratios, and are not genome‐wide. Although the addition of ChIP to 3C (ChIP–3C) would conceivably reduce noise and increase specificity for chromatin interaction detection, there are concerns that simple mixing of the ChIP and 3C protocols would lead to high levels of false positives. In this essay, we dissect current ChIP‐ and 3C‐based methodologies, discuss the models of specific as opposed to non‐specific chromatin interactions, and suggest approaches to separate specific chromatin complexes from non‐specific chromatin fragments. We conclude that the combination of sonication‐based chromatin fragmentation, ChIP‐based enrichment, chromatin proximity ligation and Paired‐End Tag ultra‐high‐throughput sequencing will be a winning implementation for genome‐wide, unbiased and de novo discovery of long‐range chromatin interactions, which will help to establish an emerging field for studying human chromatin interactomes and genome regulation networks in three‐dimensional spaces. J. Cell. Biochem. 107: 30–39, 2009. © 2009 Wiley‐Liss, Inc.     

Nuclear dreams: The malignant alteration of nuclear architecture

Cancer is diagnosed by examining the architectural alterations to cells and tissues. Changes in nuclear structure are among the most universal of these and include increases in nuclear size, deformities in nuclear shape, and changes in the internal organization of the nucleus. These may all reflect changes in the nuclear matrix, a non-chromatin nuclear scaffolding determining nuclear form, higher order chromatin folding, and the spatial organization of nucleic acid metabolism. Malignancy-induced changes in this structure may have profound effects on chromatin folding, on the fidelity of genome replication, and on gene expression. Elucidating the mechanisms and the biological consequences of nuclear changes will require the identification of the major structural molecules of the internal nuclear matrix and an understanding of their assembly into structural elements. If biochemical correlates to malignant alterations in nuclear structure can be identified then nuclear matrix proteins and, perhaps nuclear matrix-associated structural RNAs, may be an attractive set of diagnostic markers and therapeutic targets. J. Cell. Biochem. 70:172–180, 1998. © 1998 Wiley-Liss, Inc.     

The interaction of two classes of nuclear vesicles is induced by the dissociation of soluble proteins from one class of vesicles

The regulatory mechanism of fusion steps in nuclear envelope assembly was studied in vitro using cell-free extracts of Xenopus eggs. The nuclear envelope is formed only around the chromatin at the end of mitosis. Two kinds of vesicles are required for nuclear envelope assembly (J. Cell Biol. 112 (1991) 545). Light vesicles (LVs) have the chromatin-binding activity, but cannot fuse solely. On the other hand, heavy vesicles (HVs) neither bind to the chromatin nor LVs, but are needed for the fusion event. Therefore, the association of HVs with LVs that bind to the chromatin is required at a first step during the fusion of vesicles. We found that salt-treated HVs inhibited the binding of LVs to the chromatin. In addition, when salt-treated HVs were pretreated with the proteins in the residue of salt-treatment of HVs, LVs recovered the chromatin-binding activity. In contrast, salt-treatment of LVs did not influence the binding of LVs with chromatin. By using a fluorescence microscopy assay, we showed directly that salt-treated HVs associated with LVs or salt-treated LVs, but HVs did not. These results suggest that soluble mask proteins on HVs keep the two distinct vesicles separate. We propose that the dissociation of mask protein on HVs allows HVs to bind with LVs that are located on the chromatin, subsequently the fusion of each vesicle occurs and the nuclear envelope is formed.     

Matrin 3: Chromosomal distribution and protein interactions

Matrin 3 (matr3), an abundant protein of the internal nuclear matrix, has been linked to a variety of functional events. As a step toward defining its multifunctional nature, we have studied the association of matr3 with chromosome territories and identified potential interacting proteins. A similar staining pattern of matr3 was observed in fixed WI38 fibroblast cells and in live HeLa cells using a matr3‐GFP construct. Matr3 was detected throughout autosomal and the active X chromosome territories. Conversely, matr3 was strikingly excluded from the inactive X chromosome as well as within both the perinuclear and perinucleolar heterochromatin. Yeast two hybrid analysis identified matr3 interactions with 33 unique nuclear localized proteins and also revealed its propensity for self association. A majority of these proteins are involved in RNA metabolism and chromatin remodeling while others function in protein translation, DNA replication/repair and apoptosis. Further analysis of a selection of these proteins and scaffold attachment factor A (SAFA) by co‐localization and co‐immunoprecipitation experiments using HeLa cells confirmed their interactions with matr3. J. Cell. Biochem. 108: 125–133, 2009. © 2009 Wiley‐Liss, Inc.     

In vitro dynamics of chromatin organization and migration

The organization of eukaryotic chromatin is not static but changes as a function of cell status during processes such as proliferation, differentiation, and migration. DNA quantification has not been used extensively to investigate chromatin dynamics in combination with cellular migration. In this context, an optimized DNA-specific, nonperturbant method has been developed for studying chromatin organization, using the fluorescent vital bisbenzimidazole probe Hoechst 33342: this property has been described by Hamori et al. (1980). Computer-assisted image analysis was used to follow migratory activity and chromatin organization of L929 fibroblasts during in vitro wound healing. Cell movements were analyzed using an optical flow technique, which consists in the calculation of the velocity field of cells and nuclear movements in the frame. This system allows the correlation of cell migration and position in the cell cycle. It makes it possible to study chromatin dynamics using a quantitative analysis of nuclear differentiation reorganization (nuclear texture) and to correlate this with migration characteristics. The present system would be of interest for studying cell-extracellular matrix interactions using differing substrates, and also the migratory response to chemotactic factors. Such a model is a prerequisite for gaining better understanding of drug action.