Genome regulation in mammalian cells

Role of tumor invasiveness, the extracellular matrix, and chromatin sequestration in the susceptibility of uveal melanoma to herpes simplex virus type 1

To better understand determinants of susceptibility/resistance of uveal melanomas to herpes simplex virus type 1 (HSV-1) oncolytic therapy, uveal melanoma cell lines of low (OCM1a) and of high (M619, MUM2B) invasive potential were infected with HSV-1 either in the presence or absence of a laminin-rich extracellular matrix (Matrigel). OCM1a cultures were destroyed faster by HSV-1 than M619 and MUM2B cultures. In the presence of Matrigel, all melanoma cultures demonstrated delayed destruction by HSV-1 relative to Matrigel-free cultures. As sequestration of chromatin is a characteristic feature of highly invasive uveal melanomas that is further increased by exposure to laminin, we explored whether chromatin sequestration could be reversed by HSV-1 infection. HSV-1 infection induced a global reversal of chromatin sequestration in highly invasive uveal melanoma cells. However, this viral effect was first observed only 2h following virus infection and required novel protein synthesis from input viral DNA. These findings suggest that tumor invasiveness, the spatial relationship of tumor cells to laminin and chromatin sequestration are determinants of susceptibility/resistance of melanomas to HSV-1 oncolytic therapy. Furthermore, these findings indicate for the first time that HSV-1 infection is associated with global exposure of normally highly sequestered cellular DNA in malignant cells.

Chromatin organization measured by AluI restriction enzyme changes with malignancy and is regulated by the extracellular matrix and the cytoskeleton

Given that expression of many genes changes when cells become malignant or are placed in different microenvironments, we asked whether these changes were accompanied by global reorganization of chromatin. We reasoned that sequestration or exposure of chromatin-sensitive sites to restriction enzymes could be used to detect this reorganization. We found that AluI-sensitive sites of nonmalignant cells were relatively more exposed compared to their malignant counterparts in cultured cells and human tumor samples. Changes in exposure and sequestration of AluI-sensitive sites in normal fibroblasts versus fibrosarcoma or those transfected with oncogenes, nonmalignant breast cells versus carcinomas and poorly metastatic versus highly invasive melanoma were shown to be independent of the cell cycle and may be influenced by proteins rich in disulfide bonds. Remarkably, regardless of degree of malignancy, AluI-sensitive sites became profoundly sequestered when cells were incubated with laminin, Matrigel, or a circular RGD peptide (RGD-C), but became exposed when cells were placed on collagen I or in serum-containing medium. Disruption of the actin cytoskeleton led to exposure, whereas disruption of microtubules or intermediate filaments exerted a sequestering effect. Thus, AluI-sensitive sites are more sequestered with increasing malignant behavior, but the sequestration and exposure of these sites is exquisitely sensitive to information conferred to the cell by molecules and biomechanical forces that regulate cellular and tissue architecture.

Transposition of DNase hypersensitive chromatin to the nuclear periphery coincides temporally with nerve growth factor-induced up-regulation of gene expression in PC12 cells

To test the hypothesis that the nonrandom organization of the contents of interphase nuclei represents a compartmentalization of function, we examined the relative, spatial relationship of small nuclear ribonucleoproteins (snRNPs) and of DNase I hypersensitive chromatin (DHC) in rat pheochromocytoma cells. In controls, DHC and snRNPs colocalized as pan-nuclear speckles. During nerve growth factor-induced differentiation, both snRNPs and DHC migrated to the nuclear periphery with the migration of DHC preceding that of snRNPs, resulting in their transient separation. The formation of DHC shells temporally coincided with an up-regulation of neurofilament light chain mRNA. This indicates that the expression of this sequence may be associated with its spatial transposition to the nuclear periphery.

DNA exposure and condensation in the X and 21 chromosomes

Fluorescence in situ hybridization (FISH) whole chromosome painting probe studies have been carried out with X and 21 chromosomes on normal human fibroblasts grown in tissue culture. The majority of the cells were in G1 phase (including G0). The X chromosome, which exhibits differential inactivation, displays an active form which is most commonly in the nuclear periphery, is diffused over a large area with dark regions interspersed with bright regions, and exhibits punctate bright spots at its edges. The inactive X, which contains a small fraction of active genes, is also most often at the nuclear periphery, is highly condensed and also exhibits punctate labeling around its outer edge. Occasional nuclei exhibit X chromosomal material adjacent to a nucleolus. These observations fit the pattern proposed by the genome exposure theory in which inactive gene regions are sequestered by chromosome condensation, and become exposed by decondensation into a condition invisible by the video-imaging technique employed. Such exposed genes can then be activated by appropriate molecular messengers. In accordance with this theory, the total fluorescence observed from the active X is appreciably less than that of the inactive. The FISH pattern from chromosome 21 is very different, displaying two fluorescent bodies usually connected with the nucleoli. Both bodies contain condensed and decondensed regions, and both are much more similar in their degree of decondensation than was the case with the X chromosomes, although a small difference cannot be ruled out. Use of DNase I treatment of nuclei reveals the existence of exposed DNA. The use of FISH as demonstrated here can indicate sequestered DNA. Together the two techniques promise elucidation of gene regions of various chromosomes which are active and inactive in particular tissues and in normal and pathologic conditions.

Chromatin structure and the expression of cardiac genes

Actively transcribed genes are more susceptible to nuclease digestion, an observation suggested to reflect an altered state of chromatin organization. It has been hypothesized that exposure or sequestration of chromatin domains is a higher order gene regulatory mechanism. In order to test whether tissue lineage is organized by mechanisms at the level or chromatin structure, three cardiac phenotype-conferring genes (atrial natriuretic factor, myosin light chain-1-ventricular and alpha-tropomyosin) have been assessed for DNase 1 sensitivity in nuclei prepared from tissues of the developing guinea pig. These data have been related to the level of tissue mRNA expression of these genes to ascertain whether the exposed state of genes can occur when transcription is low or undetectable. Although this phenomenon was evident in some cases, the data were not consistent with mechanisms at the level of chromatin structure directing tissue type.

On the ontogeny of cardiac gene transcripts

As a prerequisite to investigating the specification and differentiation of cardiac tissue in vitro, the ontogeny of a number of putative cardiac-specific, and striated muscle-specific gene transcripts has been studied. The probes used include cDNAs of alpha-actins, myosin heavy chains, myosin light chains, alpha-tropomyosin, troponin-T and atrial natriuretic factor. The expression of these genes was monitored by Northern analysis of heart and various other tissues at three developmental ages, viz, adult, neonatal and mid-foetal. The aim of this exercise was to confirm the efficacy of a number of markers to represent a cardiac-specific subset of gene expression in our mammalian model, the guinea pig. Our results indicate predominantly cardiac expression for the mRNA transcripts of cardiac alpha-actin (c alpha-actin), cardiac myosin heavy chain-alpha (MHC alpha), cardiac myosin heavy chain-beta (MHC beta), myosin light chain-1A (MLC1A), myosin light chain-1V (MLC1V), alpha-tropomyosin (alpha TM), cardiac troponin-T (cTnT) and atrial natriuretic factor (ANF). Furthermore, cardiac-specific expression at the midfoetal time point was observed for five gene transcripts, MLC1V, MHC alpha, MHC beta, striated alpha TM and ANF. No genes were expressed exclusively in cardiac tissue; for example, expression of the genes for c alpha-actin, both cardiac MHCs, both MLCs, alpha TM and cTnT was evident in skeletal and vascular smooth muscles at some stages of development. An interesting difference between this species and those of previous studies was the minor contribution of skeletal alpha-actin to cardiac phenotype.(ABSTRACT TRUNCATED AT 250 WORDS)

On the role of lipids in cell regulatory economy

Prenylated proteins, which contain a lipid tail, may function to enhance the self-assembly of complementary molecular structures by providing a monomolecular film between the two combining regions so that electrostatic forces of attraction are greatly increased over that which would be established with water molecules in the intervening spaces. Such interactions may be important in DNA regulation, RNA processing, and a variety of protein-protein interactions.

Morphological transformation of Syrian hamster embryo cells by pseudorabies virus related growth factor

Syrian hamster embryo (SHE) clonal morphological transformation assay has been used for the in vitro testing of transforming activity of Pseudorabies virus (PRV) related growth factor (PRGF). It was found that PRGF induces morphologically transformed colonies of SHE cells in the wide titer scale (in the range 1 x 10(7) to 1 x 10(13) U/ml). The concentrations of PRGF which induced the transforming phenotype of SHE cells in the colonies did not cause significant cytotoxic effect.

Reverse transformation and genome exposure in the C6 glial tumor cell line

Reexpression of growth control and differentiation in response to physiological inducers can be demonstrated in some malignant cell lines, showing that they are not irreversibly transformed. This switch in phenotype is likely to reflect a changing pattern of gene expression, but it has not been known whether such cellular transitions involve major or only minor modulation of chromatin structure. We have studied growth control and accessibility of chromatin to DNase I in C6 glioma cells subjected to different growth regimens using an in situ nick translation assay to label the most exposed regions of nuclear chromatin. In fibroblasts and primary glia, exposed chromatin was localized mainly at the nuclear lamina. This readily labeled DNA structure was largely lacking in the malignant C6 glioma. When C6 cells were treated with dibutyryl cyclic AMP, exposed chromatin was reestablished around the nuclear periphery. This restoration of a normal genome exposure pattern required cytoskeletal integrity. Thus large-scale nuclear reorganization events proceed in parallel with phenotypic normalization. The changes in cell morphology, growth control, cytoskeletal organization, and chromatin exposure and localization are similar to the reverse transformation reaction in CHO-K1 cells, which is also regulated by the cyclic nucleotide system. Hydrocortisone and dexamethasone also restored genome exposure in C6 but less markedly than cAMP derivatives. Diverse transformed cells can thus respond to growth control stimuli with similar nuclear restructuring events, which presumably underlie changes in gene expression. Reverse transformation and redifferentiation appear to be alternative terms describing essentially the same biological phenomenon.

Reverse transformation, genome exposure, and cancer

The reverse transformation reaction whereby malignant cells are restored to a more normal phenotype has been reviewed. The primary causative action is ascribed to the genome exposure reaction in which a peripheral nuclear DNA region is restored to high sensitivity to DNase I, like that in normal cells. Various aspects of genome exposure around the nucleoli and the nuclear periphery are considered. The special role of the cytoskeleton in regulating exposure resulting in normal differentiation on the one hand and malignant transformation on the other is discussed. The action of the two-level system for regulation of the mammalian genome previously proposed is reviewed in relation to normal differentiation and malignancy with brief indication of roles played by various metabolites, transcription factors, protooncogenes, cell organelles, and processes like specific phosphorylation and dephosphorylation. Possible implications for cancer therapy and prevention and for the fields of genetic disease and toxicology are indicated.

Confocal microscopy of genome exposure in normal, cancer, and reverse-transformed cells

Genome exposure studies were carried out on malignant CHO-K1 and C6 rat glioma cells and their respective, phenotypically normal counterparts (reverse-transformed CHO-K1, and both reverse-transformed C6 glioma and normal rat fibroblasts). Cells were subjected to the nick-translation technique previously developed to make visible the exposed (i.e., DNase I-sensitive) nuclear DNA, and examined by both epifluorescence and confocal microscopy. The confocal microscopy, by permitting examination of sections throughout the nucleus, made possible clearer identification of the regions of exposed and sequestered DNA in the cells studied. A peripheral shell of exposed DNA with some discontinuities was displayed in the great majority of the cells with normal phenotype, but in none of the cancer cells. Both types of cells displayed regions of exposed DNA in the nuclear interior, particularly surrounding the nucleoli. In accordance with previous theoretical proposals we postulate: the peripheral nuclear shell of exposed DNA contains differentiation-specific genes that include the specific growth-control genes and that are functional in normal cells but not in cancer; the exposed genes surrounding the nucleoli may represent housekeeping genes active in both normal and cancer cells; and the DNase I-resistant DNA in the interior of the nucleus we postulate to consist for the most part of genes specific to alternative differentiation states and to be sequestered and inactive. Previous differences in evaluation of roles of peripheral and internal DNA sensitivity to DNAse I hydrolysis appear to be reconciled by this formulation. Identification of exposed DNA may be useful in cancer diagnosis.

Differential genomic susceptibility in malignancy correlates with changes in ATATAT DNA-binding proteins

Accesibility to DNA in the nucleus is important for the regulation of gene expression and for the effect of DNA-modifying drugs. We have now studied differential genome susceptibility in normal melanocytes and the corresponding malignant melanoma. DNA hypersensitivity assays revealed a markedly lesser degradation in melanoma nuclei compared to that in melanocytes. Cross-linking of DNA to nuclear proteins by ultraviolet light showed a cell-type dependent inverse correlation of genomic susceptibility with binding of (dA.dT) (dA.dT) sequences, compared to that shown with (dG.dC) (dG.dC), regardless of methylation in cytosines. Exposure to cholera toxin partly reversed genomic susceptibility and increased DNA/protein cross-linking in melanocytes. In contrast, melanoma cells showed decreased DNA/protein interactions and greater genome susceptibility after exposure to cholera toxin or okadaic acid. Our data suggest that a molecular mechanism for differential genome exposure in cancer cells involves a modified expression of sequence-specific DNA-binding proteins.

The spatial distribution of exposed nuclear DNA in normal, cancer, and reverse-transformed cells

The malignant CHO-K1 cell is reverse-transformed by cAMP, regaining the phenotype of a normal fibroblast. During this reaction, much of its DNA re-acquires sensitivity to hydrolysis by DNase I in a way characteristic of the normal fibroblast. Exposed DNA forms a rim about the nucleus in both the normal and reverse-transformed cell but not in the malignant CHO-K1. Reacquisition of the nuclear rim requires an organized cytoskeleton. Sequestered DNA forms families of different degrees of sequestration. In accordance with previous theoretical developments it is proposed that (i) genes specific to a given differentiation state are stored in the nuclear rim, whereas genes specific to other states are sequestered within the nucleus; (ii) only exposed genes are active, and their activity is modulated by regulatory molecules in the fluid medium; (iii) exposure and sequestration are regulated by cytoskeletal and nuclear protein structures; (iv) in at least several types of cancer the regulatory defect lies in the genome exposure process so that the specific DNA sequences and their associated growth regulatory loci have been transferred from the exposed to the sequestered condition with consequent loss of the nuclear rim of exposed DNA. The methodology described should be generally applicable to examining the accessibility state of subsets of DNA during various physiological modulations of cell function.