Ronald Hancock

A new look at the nuclear matrix.

Abstract.The concept of the nuclear matrix, a karyoskeletal structure that serves as a support for the genome and its activities, has stimulated many studies of the association of nuclear components and functions with this structure. However, certain experimental findings are not consistent with the existence of the nuclear matrix in vivo, including our inability to visualise a corresponding structure in intact cells, the demonstrated mobility in vivo of chromatin and messenger ribonucleoprotein particles, which are claimed to be bound to the nuclear matrix, the paradoxical extractability from nuclei in low ionic strength buffers of enzymes that are found in the 2 M NaCl-insoluble matrix, and the extractability, in conditions which reproduce the intranuclear milieu, of regions of DNA (matrix or scaffold attachment regions, MAR/SARs) postulated to be bound to the nuclear matrix in vivo. This review considers the nuclear matrix model in the light of sometimes overlooked evidence that each step in its isolation may cause nuclear components to bind to it by new liaisons that do not exist in vivo. This is illustrated by experiments where nuclear-targeted green fluorescent protein is found in the nuclear matrix, and raises the possibility that MAR/SARs actually bind to DNA-binding proteins or multiprotein complexes, including replicational, transcriptional and processing machinery, and topoisomerases that are incorporated into the nuclear matrix during its preparation. Considering that the nuclear lamina forms a rigid exoskeleton, the necessity for internal skeletal structures is raised; the major roles that macromolecular crowding, phase partitioning, and charge effects are likely to play in organisation of the intranuclear space may provide new models for the compartmentalisation of proteins and functions into different nuclear domains and of chromosomes into territories.

Internal organisation of the nucleus: assembly of compartments by macromolecular crowding and the nuclear matrix model

Abstract Many and possibly all macromolecules in the nucleus are segregated into discrete compartments, but the current model that this is achieved by a fibrillar nuclear matrix which structures the nuclear interior and compartments is not consistent with all experimental observations, as reviewed here. New results are presented which suggest that macromolecular crowding forces play a crucial role in the assembly of at least two compartments, nucleoli and PML bodies, and an in vitro system in which crowding assembles macromolecular complexes into structures which resemble nuclear compartments is described. Crowding forces, which are strong in the nucleus due to the high macromolecule concentration (in the range of 100 mg/ml), vastly increase the association constants of intermolecular interactions and can segregate different macromolecules into discrete phases. The model that they play a role in compartmentalisation of the nucleus is generally consistent with the properties of compartments, including their spherical or quasispherical form and their dynamic and mobile nature.

Influence of Polymorphisms in DNA Repair Genes XPD, XRCC1 and MGMT on DNA Damage Induced by Gamma Radiation and its Repair in Lymphocytes In Vitro

Abstract Rzeszowska-Wolny, J., Polanska, J., Pietrowska, M., Palyvoda, O., Jaworska, J., Butkiewicz, D. and Hancock, R. Influence of Polymorphisms in DNA Repair Genes XPD, XRCC1 and MGMT on DNA Damage Induced by Gamma Radiation and its Repair in Lymphocytes In Vitro. Radiat. Res. 164, 132– 140 (2005). DNA single-strand breaks (SSBs) were quantified by single-cell gel electrophoresis and micronucleated and apoptotic cells were quantified by microscopic assays in peripheral blood lymphocytes after irradiation on ice with 2 Gy of 60Co γ radiation, and their association with polymorphisms of genes that encode proteins of different DNA repair pathways and influence cancer risk (XPD codon 312Asp → Asn and 751Lys → Gln, XRCC1 399Arg → Gln, and MGMT 84Leu → Phe) was studied. In unirradiated lymphocytes, SSBs were significantly more frequent in individuals older than the median age (52 years) (P = 0.015; n = 81), and the frequency of apoptotic or micronucleated cells was higher in individuals with alleles coding for Asn at XPD 312 or Gln at 751 (P = 0.030 or 0.023 ANOVA, respectively; n = 54). The only polymorphism associated with the background SSB level was MGMT 84Phe (P = 0.04, ANOVA; n = 66). After irradiation, SSB levels and repair parameters did not differ significantly with age or smoking habit. The SSB level varied more than twofold and the repair rate and level of unrepaired SSBs more than 10-fold between individuals. The presence of variant alleles coding for Asn at XPD 312 was associated with more radiation-induced SSBs (P = 0.014) and fewer unrepaired SSBs (P = 0.008), and the phenotype (>median induced SSBs/<median unrepaired SSBs) was seen in the majority of XPD 312Asn/Asn homozygotes; the odds ratio for variant homozygotes to show this phenotype was 5.2 (95% confidence interval 1.4–19.9). The hypothesis is discussed that XPD could participate in repair of ionizing radiation-induced DNA damage. While it cannot be excluded that the effects observed are due to cosegregating polymorphisms or that the responses of lymphocytes are not typical of other cell types, the results suggest that polymorphism of DNA repair genes, particularly XPD, is one factor implicated in the variability of responses to ionizing radiation between different individuals.

Nuclear matrix attachment regions and topoisomerase II binding and reaction sites in the vicinity of a chicken DNA replication origin

We have mapped nuclear matrix attachment regions (MARs), defined by their specific binding to nuclear matrices in vitro, and sites of topoisomerase II reaction, detected by DNA cleavage in vitro in the presence of the inhibitor VM-26, in the vicinity of the replication origin of the chicken alpha-globin gene domain. Two MARs are located close to the downstream end (in the direction of transcription) of a 3 kb fragment which includes the origin. These MARs contain sites for strong topoisomerase II binding and reaction. Our observations on this gene domain support two hypotheses concerning MARs in eukaryotic cells, namely that they are close to DNA replication origins and that they contain multiple topoisomerase II recognition sites.

Chromosome recombination and defective genome segregation induced in Chinese hamster cells by the topoisomerase II inhibitor VM-26

We found that 4′-demethylepipodophyllotoxinthenylidene-β-d-glucoside (VM-26; Teniposide), which specifically inhibits the enzyme DNA topoisomerase II, induces the formation of quadriradial chromosomes in Chinese hamster ovary cells. VM-26 traps topoisomerase II molecules when they are covalently integrated into DNA during their reaction. Quadriradial chromosomes are formed by reciprocal exchange of double-stranded DNA between single chromatids of two different chromosomes. Using synchronised cells, we found that they were formed after a single replication cycle in the presence of VM-26 at a low concentration (0.008μM), which does not affect DNA replication, and occurred in 50% of the mitotic cells at a concentration of 0.16 μM. They were also formed when VM-26 was present for only 1.5 h before mitosis, after the completion of S-phase DNA replication. Chromatids bearing a translocated segment of another chromatid, which were derived from recombined chromosomes, were observed in late metaphase cells. Segregation of the daughter genomes was defective in many mitotic cells, probably because chromatids with two or no centromeres and kinetochores, formed from chromosomes recombined between their centromeres, could not be segregated. In the light of evidence that topoisomerase II molecules covalently integrated in DNA are trapped and therefore more abundant in the presence of VM-26, and that this enzyme can effect recombination of double-stranded DNA in vitro, we interpret these observations as evidence that topoisomerase II can mediate chromosome recombination in vivo.

An antigen located in the kinetochore region in metaphase and on polar microtubule ends in the midbody region in anaphase, characterised using a monoclonal antibody

We describe a new component of the kinetochore region of Chinese hamster ovary cells, which was characterised using a monoclonal antibody (mAb). This antigen was localised on the kinetochore regions of purified metaphase chromosomes, but in anaphase it was instead located on the polar microtubules in the midbody region, where they terminate in the stembody. It was not detectable in prophase or interphase cells by immunofluorescence, but was present in the interphase nucleus as shown by immunoblotting after SDS-polyacrylamide gel electrophoresis. The mAb recognised two polypeptides of Mr 140 000 and 155 000. The localisation of this antigen in metaphase on the kinetochore region, where the plus ends of the kinetochore microtubules are temporarily stabilised when they attach, and later in the stembody and midbody where the plus ends of the polar microtubules are stabilised in anaphase and telophase, suggests that it could play a role in stabilising the plus ends of microtubules and thus in the control of microtubule dynamics during mitosis.

Bystander Effects Induced by Medium From Irradiated Cells: Similar Transcriptome Responses in Irradiated and Bystander K562 Cells

PURPOSEnCells exposed to ionizing radiation release factors that induce deoxyribonucleic acid damage, chromosomal instability, apoptosis, and changes in the proliferation rate of neighboring unexposed cells, phenomena known as bystander effects. This work analyzes and compares changes in global transcript levels induced by direct irradiation and by bystander effects in K562 (human erythroleukemia) cells.nnnMETHODS AND MATERIALSnCells were X-irradiated with 4 Gy or transferred into culture medium collected from cells 1 h after irradiation (irradiation-conditioned medium). Global transcript profiles were assessed after 36 h of growth by use of Affymetrix microarrays (Affymetrix, Santa Clara, CA) and the kinetics of change of selected transcripts by quantitative reverse transcriptase-polymerase chain reaction.nnnRESULTSnThe level of the majority (72%) of transcripts changed similarly (increase, decrease, or no change) in cells grown in irradiation-conditioned medium or irradiated, whereas only 0.6% showed an opposite response. Transcript level changes in bystander and irradiated cells were significantly different from those in untreated cells grown for the same amount of time and were confirmed by quantitative reverse transcriptase-polymerase chain reaction for selected genes. Signaling pathways in which the highest number of transcripts changed in both conditions were found in the following groups: neuroactive ligand-receptor, cytokine-cytokine receptor interaction, Janus Kinase-Signal Transducers and Activators of Transcription (JAK-STAT) and Mitogen-Activated Protein Kinase (MAPK) In control cells more transcripts were downregulated than in irradiated and bystander cells with transcription factors YBX1 and STAT5B, heat shock protein HSPA1A, and ribonucleic acid helicase DDX3X as examples.nnnCONCLUSIONSnThe transcriptomes of cells grown in medium from X-irradiated cells or directly irradiated show very similar changes. Signals released by irradiated cells may cause changes in the transcriptome of neighboring cells that sustain their survival.

Structure of Metaphase Chromosomes: A Role for Effects of Macromolecular Crowding

In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ∼30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100–200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ∼30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.

X-irradiation and bystander effects induce similar changes of transcript profiles in most functional pathways in human melanoma cells.

Unirradiated cells which neighbor cells exposed to ionizing radiation (IR) show responses termed bystander effects, including DNA damage, chromosomal instability, mutation, and apoptosis. We used genome-wide microarrays to compare the change in transcript profiles in Me45 (human melanoma) cells grown in culture medium from irradiated cells (irradiation conditioned medium, ICM) with those which occurred after IR, sampling after more than one division cycle to detect long-term changes which could be relevant in radiotherapy. Transcripts of >10,000 genes showed an increased or decreased level in both conditions using the criterion of a >+/-10% change, and >85% of these were common to growth in ICM and after IR. When these genes were grouped into metabolic pathways according to the Kyoto Encyclopedia of Genes and Genomes (KEGG), significant differences (p<0.01) were seen between the numbers of up- and down-regulated transcripts in certain groups after both ICM and IR, particularly in the groups neuroactive ligand-receptor interactions, oxidative phosphorylation, cytokine-cytokine receptor interactions, proteasomes, and ribosomes. Quantitative RT-PCR assays of transcripts of selected genes in these pathways confirmed the similar effects of growth in ICM and IR. We conclude that factors transmitted from irradiated cells can influence transcript levels in bystander cells, and that these changes persist for more than one cell cycle consistent with the long-term transmissible effects seen in progeny cells, revealing new facets of the IR-induced bystander effect.

The Crowded Nucleus

The principles that determine the organization of the nucleus have become clearer in recent years, largely because of new insights into polymer, colloid, and soft-matter science. Macromolecules, together with the giant linear polymers that form the chromosomes, are confined at high concentrations within the nuclear envelope and their interactions are influenced strongly by short-range depletion or entropic forces which are negligible in dilute systems, in addition to the more familiar van der Waals, electrostatic, steric, hydrogen bonding, and hydrophobic forces. The studies described in this volume are consistent with the model that this complex and concentrated mixture of macromolecules is maintained in a delicate equilibrium by quite simple although unsuspected physicochemical principles. The sensitivity of this equilibrium to perturbation may underlie the controversies about the existence of a nuclear matrix or scaffold. In this volume, we underline the importance for cell biologists of being familiar with current work in colloid, polymer, soft matter, and nanoscience. This chapter presents a brief background to the aspects of the nucleus that are considered in detail in subsequent chapters.