Transcriptional Activation of Pericentromeric Satellite Repeats and Disruption of Centromeric Clustering upon Proteasome Inhibition.

Heterochromatinisation of pericentromeres, which in mice consist of arrays of major satellite repeats, are important for centromere formation and maintenance of genome stability. The dysregulation of this process has been linked to genomic stress and various cancers. Here we show in mice that the proteasome binds to major satellite repeats and proteasome inhibition by MG132 results in their transcriptional de-repression; this de-repression is independent of cell-cycle perturbation. The transcriptional activation of major satellite repeats upon proteasome inhibition is accompanied by delocalisation of heterochromatin protein 1 alpha (HP1α) from chromocentres, without detectable change in the levels of histone H3K9me3, H3K4me3, H3K36me3 and H3 acetylation on the major satellite repeats. Moreover, inhibition of the proteasome was found to increase the number of chromocentres per cell, reflecting destabilisation of the chromocentre structures. Our findings suggest that the proteasome plays a role in maintaining heterochromatin integrity of pericentromeres.

Satellite DNA spatial localization and transcriptional activity in mouse embryonic E-14 and IOUD2 stem cells.

The formation of heterochromatin begins in the differentiating cells. The aim of this work was to study changes of satellite DNA distribution, transcriptional activity and interaction with certain proteins in mouse embryonic stem cells after induction with retinoic acid. We found that pericentromeric satellites entered chromocenters only some days after induction of E-14 and IOUD2 mouse embryonic stem cells. The redistribution was accompanied by association with HP1a and transcription from pericentromeric (but not centromeric) satellite DNA. RNA was polyadenylated and transcribed from the forward chain. Probes made from the cDNA hybridized to all chromosomes. In differentiating cells, the transcript was found exclusively in chromocenters while in differentiated cultured L929 cells it formed 1-2 large clusters outside chromocenters. Using ChIP and immunostaining, we demonstrated that in induced cells pericentromeric DNA interacted with RNA-helicase p68 that was previously shown to be involved in transcription regulation and to be involved in differentiation processes.

Region-specific chromatin decondensation and micronucleus formation induced by 5-azacytidine in human TIG-7 cells.

A human diploid lung fibroblast cell strain, TIG-7, has a heteromorphic chromosome 15 with an extra short arm carrying a homogeneously staining region (15p+hsr). We demonstrated previously that the 15p+hsr consists of an inactive and G+C-rich rDNA cluster characterized by fluorescence in situ hybridization (FISH) and various chromosome banding techniques. Thus, it was suggested that the region could contain highly methylated DNA. To observe methylation status on the target region directly under the microscope, we used a demethylating agent, 5-azacytidine (5-azaC), to induce decondensation of the chromatin containing methylated DNA. At 24 h after treatment with 0.5 microM 5-azaC, marked decondensation of the 15p+hsr was observed in almost all of the metaphases. Furthermore, we observed micronuclei, which were equivalent to the rDNA of the 15p+hsr demonstrated by FISH in the same preparation. In contrast, the DNA cross-linking agent mitomycin C (MMC) preferentially induced 15p+hsr-negative micronuclei. These findings indicated that chromatin decondensation and subsequent DNA strand breakage induced by the demethylating effect of 5-azaC led specifically to 15p+hsr-positive micronuclei.

Analysis of integrated hepatitis B virus DNA and flanking cellular sequence by inverse polymerase chain reaction.

Although hepatitis B virus (HBV) DNA has been detected in the human hepatoma cell line, HAGS 2.1, viral and cellular junction sequences have not been investigated fully. To facilitate the analysis of HBV DNA integration sites in HAGS 2.1 cells, a combination of conventional polymerase chain reaction (PCR) and inverse PCR (IPCR) was carried out to identify the junction between the viral and the cellular gene. The HBV integrant and its cellular counterpart sequence were cloned and analyzed. The sequencing data indicated that the breakpoints on the HBV integrant are at nucleotide 2111 of the C gene and nucleotide 1558 of the X gene. The length of the integrated HBV DNA in HAGS 2.1 was approximately 2.6 kb, which includes partial C, P, and X genes and an intact S gene. The cellular sequence flanking the integrated HBV gene was very similar to a human satellite III repetitive sequence with 43 and 56 of GGAAT repeats on the left- and right-hand side, respectively. Although the findings on the viral-cellular junction in HAGS 2.1 cells cannot explain the liver tumorigenesis, the current study shows that by choosing the nearest restriction site, which can be determined by conventional PCR rather than using a unique site within the integrated viral sequence to do IPCR, gives a higher successful rate for cloning and the subsequent analysis of the viral-cellular junctions.

Chromatin opening of DNA satellites by targeted sequence-specific drugs.

There are few tools available for dissecting and elucidating the functions of DNA satellites and other nongenic DNA. To address this, we have explored the experimental potential of DNA sequence-specific drugs containing pyrrole and imidazole amino acids (polyamides). Compounds were synthesized that target different Drosophila melanogaster satellites. Dimeric oligopyrroles were shown to target the AT-rich satellites I, III, and SARs (scaffold associated regions). One polyamide (P31) specifically binds the GAGAA satellite V. Specificity of targeting was established by footprinting, epifluorescence of nuclei, and polytene chromosomes stained with fluorescent derivatives. These polyamides were shown to mediate satellite-specific chromatin opening of the chromatin fiber. Remarkably, certain polyamides induced defined gain or loss-of-function phenotypes when fed to Drosophila melanogaster.

Biological effects of a bifunctional DNA crosslinker. I. Generation of triradial and quadriradial chromosomes.

Interduplex crosslinks by a bifunctional anthramycin DNA crosslinker produced triradial and quadriradial chromosomes. The crosslinker alkylates guanine at N-2. Bovine chromosomes contain GC-rich density satellite DNAs at the centromeric heterochromatin and is the basis for the formation of triradial and quadriradial chromosomes at the centromeres. The in situ crosslinking of interphase chromosomes indicates that the distance between centromeres is 17.5 A. We conclude that the nuclear matrix associated DNA in the centromeric heterochromatin of interphase chromosomes are positioned close enough for crosslinking to occur. We propose a model for the generation of triradial and quadriradial chromosomes based upon the number of interduplex crosslinks between two chromosomes.

Biological effects of a bifunctional DNA cross-linker. II. Generation of micronuclei and attached micronuclear-like structures.

Madin-Darby bovine kidney (MDBK) cells were treated with the bifunctional DNA cross-linker, L-7, to examine the generation of micronuclei and other nuclear abnormalities. The preceding paper demonstrates that L-7 treatment induces the formation of triradial and quadriradial chromosomes in MDBK cells. These chromosomes are believed to result from interduplex DNA cross-links formed between G-C rich centromeric satellite DNA regions on non-sister chromatids. Treatment produces a majority of centromere-positive micronuclei. In addition, many daughter cells remain attached by chromatin bridges which are sometimes beaded with micronuclei. Up to 15% of cell nuclei become lobular and fused with numerous micronuclear-like structures attached to their membranes. These attached structures are classified as attached micronuclear-like structures (AMNLS). Fluorescence in situ hybridization (FISH) using a centromeric satellite sequence was performed on treated cells. Hybridization reveals that intercellular bridges are composed of centromeric sequences and initiate at centromeric foci in daughter cells. Furthermore, the majority of junctions between AMNLS and nuclei contain an enhancement of centromeric signal. The frequency of AMNLS appears dependent on the concentration of L-7 and the duration of treatment. Similar results were found for the generation of cross-linked chromosome products in the previous paper. We suggest that AMNLS result from the abnormal mitotic segregation of cross-linked chromosome products.

Monitoring for induced heritable mutations in natural populations: application of minisatellite DNA screening.

The need to understand the role that anthropogenic chemicals play in generating germline mutations is critical, both from an ecological and a human health perspective. Exposure to complex mixtures of urban and industrial chemicals is widespread and we have little understanding of the long-term implications to populations and gene pools. It has recently been suggested that minisatellite DNA mutations may be sensitive biomarkers for induced heritable mutations in populations exposed to radioactive and non-radioactive contamination in their environments. Minisatellite loci are attractive targets for mutational analyses because they undergo a rate of mutation much greater than unique sequence DNA and with DNA fingerprinting many loci can be scanned simultaneously. As a result, the technique is statistically powerful requiring relatively small sample sizes (compared to other in situ mutation assays) and is reasonably cost and time efficient. This paper will review the application of minisatellite mutation screening to the field of genetic toxicology.

Induction of minisatellite mutation in NIH 3T3 cells by treatment with the tumor promoter okadaic acid.

Okadaic acid (OA) is a strong tumor promoter of mouse skin carcinogenesis and also a potent inhibitor of serine/threonine protein phosphatases. OA induces various genetic alterations in cultured cells, such as diphtheria-toxin-resistance mutations, sister chromatid exchange, exclusion of exogenous transforming oncogenes, and gene amplification. The present study revealed that it caused minisatellite mutation (MSM) at a high frequency in NIH 3T3 cells, although no microsatellite mutation was found. Nine of 31 clones (29%) exhibited MSM after 6 days of OA treatment, as opposed to only 1 of 30 clones (3%) without OA exposure. Moreover, NIH 3T3 cells treated with OA acquired tumorigenicity in nude mice, giving rise to 7 tumors within 25 weeks in 20 sites where 3 x 10(6) cells were injected. In contrast, the same numbers of untreated cells gave rise to only one tumor, and the tumor grew much slower. All of three OA-induced tumors examined manifested the MSM. The findings thus point to a molecular mechanism by which OA could function as a tumor promoter, and also the biological relevance of the induction of MSM in the tumorigenic process by OA.

Nuclease susceptibility of the rat liver satellite DNA-containing chromatin decreases with age.

Nuclease susceptibility of the satellite DNA-containing chromatin of the liver of young (18 +/- 2 weeks) and old (100 +/- 5 weeks) rats was analysed using nick-translated rat 185 bp satellite I DNA fragment cloned in pBR322. With increasing concentration of DNaseI and micrococcal nuclease (MNase), multimeric forms of the satellite ladder gradually disappear in both the ages. The rate of disappearance is faster in young rats as compared to old ones. Such age-dependent decrease in the susceptibility of satellite DNA-containing chromatin reflects its condensation towards heterochromatization in old age.

Enhancement of genomic instability by 17beta-estradiol in minisatellite sequences of X-ray-transformed mouse 10T1/2 cells.

The female hormone 17beta-estradiol is involved in the development of breast cancer, an effect usually attributed to its capacity to stimulate the replication of preneoplastic and malignant cells. In this study, we report that 17beta-estradiol enhances the onset of genomic rearrangements, a type of genomic instability, in minisatellite sequences of malignant 10T1/2 mouse cells. Two malignant clones, X-ray-9 and F-17a, previously transformed in vitro by X-rays (600 cGys), and two non-transformed 10T1/2 mouse cell subclones (10T1/2b and 10T1/2c) were divided into two groups. The first group was incubated in the presence of 10(-5) M of 17beta-estradiol (dissolved in ethanol) for 5 days, while the second group was incubated for the same period in culture media containing 0.1% of ethanol. After the incubation both groups of cells were then subcloned, and their DNA was extracted and analyzed with the DNA fingerprinting assay using the probe M (core sequence: 5'-AGGC). A high frequency of genomic rearrangements was observed in the transformed subclones treated with 17beta-estradiol. Nine deletions or additions in minisatellite alleles were observed in six F-17a subclones, while 28 of those genomic rearrangements were found in the 12 X-ray-9 malignant subclones. On the other hand, for the non-transformed 10T1/2b and 10T1/2c cells, no genomic rearrangements were induced by the hormone. After the withdrawal of 17beta-estradiol from the transformed clone X-ray-9, no new genomic rearrangements were detected; while a second incubation with the hormone induced new deletions or additions in minisatellite alleles. This preferential enhancement of genomic instability in malignant 10T1/2 mouse cells suggests that 17beta-estradiol may accelerate the accumulation of mutations, and therefore may represent a mechanism by which the female hormone contributes to breast cancer development.

Inhibition of RNA polymerase II transcription causes chromatin decondensation, loss of nucleolar structure, and dispersion of chromosomal domains.

Fluorescence in situ hybridization and immunofluorescence have been used to visualize specific genomic DNA sequences and proteins in interphase nuclei treated with transcriptional inhibitors. The adenosine analog 5,6-dichloro-beta-D-ribofuranosylbenzimidazole (DRB) and alpha-amanitin selectively inhibit transcription by RNA polymerase II at low doses. Upon exposure to DRB or alpha-amanitin the fibrillar components of the normally compact nucleolus unravel into necklace-like structures which represent highly extended linear arrays of ribosomal (r)RNA genes. Similarly, blocks of tandemly repeated satellite DNAs dissociate into extended beaded strands. Localized (euchromatic) chromosome domains and even whole chromosome territories disperse throughout the nuclear interior. Treatment of cells with actinomycin D (AMD) at doses that block rRNA synthesis does not cause significant decondensation of nucleolar, heterochromatic, and interphase chromosome domains. Interestingly, both alpha-amanitin and AMD cause coilin to associate with the nucleolar domain. In AMD-treated cells, coilin is enriched in nucleolar caps abutting upon the residual nucleolus. After alpha-amanitin treatment, coilin is concentrated in numerous beads closely associated with individual rDNA transcription units within nucleolar necklaces. The changes in higher-order nuclear structure are reversible in cell cultures exposed to nontoxic doses of transcriptional inhibitors. It therefore may be concluded that nuclear topographic organization is dependent on a continued transcription of nuclear genes, but not of the rRNA genes.

Microsatellite instability, apoptosis, and loss of p53 function in drug-resistant tumor cells.

We have examined microsatellite instability and loss of p53 function in human tumor cell line models of acquired anticancer drug resistance. We observe acquisition of an RER(+) phenotype in cell lines selected for resistance to cisplatin or doxorubicin. The majority of independent cisplatin-resistant sublines are RER(+), whereas the parental line shows no evidence of microsatellite instability. Microsatellite mutations in random, nonselected subclones of a cislatin-resistant line are observed in the absence of further drug exposure, suggesting that the RER(+) phenotype is a stable phenotype rather than being transiently induced by DNA damage. Furthermore, a cisplatin-resistant derivative shows reduction in a G:T mismatch recognition activity compared to the parental line. Independent lines selected by multiple exposure to cisplatin show resistance factors of up to a 5-fold by clonogenic assay and have reduced cisplatin-induced apoptosis. The resistant lines that are RER(+) show evidence of loss of p53-dependent functions, as measured by a loss of radiation-induced G(1) arrest and reduced CIP1 mRNA. Induced loss of p53 function by transfection of mutant TP53 does not cause a detectable RER(+) phenotype. We speculate that tolerance of DNA damage and expansion of cells with an RER(+) phenotype may select for reduced ability to engage apoptosis and loss of p53 function.

Treatments with saline solutions and DNase I have different effects on DNA content and distribution in human and in mouse chromosomes.

The aim of this work was to re-examine, on a quantitative basis, the relationship between banding pattern after Giemsa staining and the amount (and distribution) of DNA along the length of the chromatid arms. To do this, we investigated by cytofluorometric methods the occurrence of possibly different extraction of chromosome DNA after some alternative G-banding procedure, i.e. treatment of chromosomes with saline solutions, or DNasi I digestion in situ. The G-banding procedure entailing trypsin pretreatment is known to be difficult to standardize; in the present investigation, it was also found that trypsin induced a massive, although quantitatively variable, extraction of DNA from fixed metaphase chromosomes. G-banding-like patterns may be obtained, by treating chromosomes preparations with saline solutions. Both PBS and Tris-HCl treatment for the times considered induced a G-banding-like pattern after Giemsa staining, regardless of the age of chromosome preparations; no banding was observed after staining DNA with PI, nor extraction of DNA was found to occur. DNase I digestion initially induced a G-banding in both human and mouse chromosomes after Giemsa staining, with concomitant extraction of DNA (but without apparent G-banding-like pattern after PI staining); after 30 min digestion, a C-banding-like pattern was observed after both Giemsa and PI staining. Exposure to PBS or Tris-HCl buffer at room temperature may therefore be recommended as a G-banding inducing treatment, since it allows the classification of single chromosomes after Giemsa staining, without determining significant displacement of genomic DNA, which can be submitted to further analysis in situ.

Microsatellite alterations in human and rat esophageal tumors at selective loci.

(CA)n simple repeats in DNA were examined at 17 loci in 18 human squamous cell carcinomas of the esophagus and compared with those in normal esophageal tissue from the same patients. Six loci were examined in 32 esophageal papillomas that had been induced by N-nitrosomethylbenzylamine in BD VI rats. Length-altered CA repeats were found in two human tumors and four rat papillomas. Loss of heterozygosity was observed in three human tumors; two rat papillomas had lost microsatellite bands that are common in inbred BD VI rats. Both (CA)n microsatellite length alteration and loss of heterozygosity were clustered at certain loci in the human tumor samples and in the chemically induced rat esophageal tumors. Our findings indicate that genomic instability that results in alteration of repeated sequences not only occurs in human tumors but may also be a consequence of chemical carcinogenesis in rodents.

Induction of minisatellite DNA rearrangements by genotoxic carcinogens in mouse liver tumors.

We investigated whether somatic rearrangements in minisatellite DNA are more frequent in chemically induced mouse liver tumors than they are in spontaneous tumors. CD-1 mouse liver tumors were induced by either a single dose or 15 consecutive daily doses of 7,12-dimethylbenz[alpha]anthracene, 4-aminoazobenzene, N-hydroxy-2-acetyl-aminofluorene or diethylnitrosoamine (DEN). Using DNA fingerprinting analysis, we found that the single- and multiple-dose carcinogen treatments caused a 2- to 5-fold higher frequency of minisatellite DNA rearrangements compared with that found in spontaneous tumors--with the exception of single-dose DEN tumors, which showed no increase in rearrangements. Our results suggest that DNA fingerprinting may be a valuable assay for differentiating certain chemically induced tumors from spontaneous tumors.

Specific induction of uncoiling in NORs of human acrocentric chromosomes by 5-azacytidine and 5-azadeoxicytidine.

The organization of rDNA-containing chromatin was analysed by transmission electron microscopy after treatment of cultured human lymphocytes with 5-azacytidine (ACR) or 5-azadeoxicytidine (AdCR). The number of observed acrocentric chromosomes with satellites was significantly increased after treatment with low doses of ACR or AdCR during the last 24 h of culture, whereas with exposures during the last 7 h the number remained normal. The results suggest that the incorporation of ACR and AdCR in the early period of the S-phase may have reverted the non-satellized to satellized chromosomes. The cytidine analogues may have become more visible during secondary constriction thus changing the NOR structure leading to an increased number of satellized chromosomes.

Human alpha-satellite DNAs are not susceptible to undercondensation after 5-azacytidine treatment.

Localization of alphoid human satellite DNAs using fluorescence in situ hybridization (FISH) of metaphase chromosomes following treatment with 5-azacytidine to produce undercondensation showed that human alpha-satellite DNA is not sensitive to the condensation-inhibition effect of 5-azacytidine. The difference in heterochromatic DNA subsets was particularly evident in the constitutive heterochromatin of chromosomes 1 and 9. Comparison of the results obtained after FISH with those obtained from electron microscopy and G-banding enabled accurate localization of this DNA domain.

Chemically induced changes in the spectrum of amplifications of the human minisatellite MS1 integrated in chromosome III of a haploid yeast strain.

To study chemically induced DNA amplifications we used the haploid Saccharomyces cerevisiae strain TR(MS1)-1 carrying an integrated chromosomal copy of the human minisatellite. MS1. Chemicals with different mechanisms of action were tested in this strain: methyl methanesulphonate, ethylene oxide (EO), propylene oxide (PO), camptothecin, 2,3,7,8-tetrachlorodibenso-p-dioxin (TCDD) and reserpine. No increase in frequency of new MS1 length alleles was seen with any of the tested chemicals relative to the spontaneous frequency of approximately 30%. EO and TCDD induced changes in the amplification spectrum, i.e., the frequency distribution of MS1 length alleles longer than the original 1.42 kb allele. PO and camptothecin increased the frequency of plasmid "pop-out" events. It seems likely that several mechanisms e.g. unequal exchanges, replication slippage and loop formation leading to deletion of a ring of tandem repeats, are involved in the generation of new MS1 length alleles. A loop-forming deletion mechanism is supported by the tendency to multimodality shown in the deamplification (loss of repeat units) spectra, i.e. the frequency distribution of new MS1 length alleles shorter than the original allele. EO and TCDD induced "longer" MS1 length alleles as compared to the control. The frequent generation of new MS1 length alleles in this haploid yeast strain further demonstrates the instability of such sequences and their possible relevance to genetic toxicology and the mechanisms of induction of cancer as well as other diseases. This study is a first step towards the development of an assay for DNA amplification without the use of a selective agent.

Influence of amsacrine (m-AMSA) on bulk and gene-specific DNA damage and c-myc expression in MCF-7 breast tumor cells.

In the MCF-7 human breast tumor cell line, the aminoacridine, m-AMSA, induces protein-associated DNA strand breaks consistent with inhibition of topoisomerase II. However, neither single-strand nor double-strand breaks in DNA, determined using conventional assays, show a consistent relationship with m-AMSA-induced inhibition of growth. In contrast, when DNA strand breaks are determined by alkaline unwinding under the high salt conditions of the alkaline unwinding/Southern blotting (AU/SB) assay, developed by our laboratories, damage to DNA corresponds closely with growth inhibition. The AU/SB assay, which is capable of assessing breaks within large-scale domains (upwards of 1 megabase) surrounding genes of interest, was further utilized to explore the capacity of m-AMSA to induce damage within specific genomic regions that may regulate cell growth. Regions encompassing the transcriptionally active oncogenes, c-myc and c-fos, were found to be more susceptible to m-AMSA-induced strand breaks than the region encompassing the non-transcribed alpha-satellite DNA or the genome as a whole (bulk DNA). These findings demonstrate that m-AMSA may produce more pronounced damage within specific genomic regions than in bulk DNA, m-AMSA also preferentially altered expression of the c-myc oncogene; at an m-AMSA concentration where growth was inhibited by between 70 and 80%, steady-state c-myc mRNA levels declined to approximately 10-15% of control levels within 2-3 hr; furthermore, concentration-dependent reductions in c-myc expression appeared to coincide with growth inhibition. In addition, inhibition of [3H]thymidine incorporation after 2 hr directly paralleled inhibition of growth, suggesting an early effect at the level of DNA biosynthesis, possibly related to the down-regulation of c-myc expression. It is proposed that specific lesions, e.g., in regions surrounding the c-myc gene, as well as generalized lesions in DNA may lead to growth inhibition mediated by down-regulation of the expression of select growth regulatory genes, such as c-myc.