To investigate the mechanism by which UV irradiation causes S-phase-dependent chromosome aberrations and thereby genomic instability, we have developed an assay to study the DNA structure of replication forks (RFs) in UV-irradiated mammalian cells, using pulse-field gel electrophoresis for the DNA analysis. We demonstrate that replication stalling at UV-induced pyrimidine dimers results in the formation of single-strand DNA (ssDNA) regions and incomplete RF structures. In normal and in excision-repair-defective xeroderma pimentosum (XP) cells, stalling at dimers is rapid and prolonged and recovery depends on dimer repair or bypass. By contrast, XP variant (XPV) cells, defective in replication of a UV-damaged template due to mutation of bypass-polymerase ?, fail to arrest at dimers, resulting in a much higher frequency of ssDNA regions in the stalled RFs. We show that the stability of UV-arrested RFs depends directly on functional p53, and indirectly on NER and pol ?. In p53-deficient cells, the stalled sites give rise to double-strand DNA breaks (DSBs), at a frequency inversely correlated with repair capacity of the cell. In normal cells only a fraction of the stalled sites give rise to DSBs, while in XPASV, XPDSV and also XPVSV all the sites do. XPVSV cells, although repair proficient, accumulate almost double the number of DSBs, suggesting that a high frequency of ssDNA regions in UV-arrested forks cause RF instability. These replication-associated DSBs do not accumulate in p53-proficient human cells. We propose that a major mechanism by which p53 maintains genome stability is the prevention of DSB accumulation at long-lived ssDNA regions in stalled-replication forks.Supplemental material for this paper can be found at the following link: http://www.landesbioscience.com/journals/cc/squiresCC3-12-sup.pdf

Damaged nucleotides are removed from the condensed non-coding, or transcriptionally inactive regions of the genome by the relatively slow global genome repair system. Since few data are available for the repair of the pericentric heterochromatin region our aim was to study the repair of a specific sequence, known to be located in this region. We applied a PCR based method to monitor UV damage and repair in chAB4, a human pericentromeric heterochromatin sequence in 10 human cell lines. We here present evidence that excision repair of a sequence in the pericentromeric heterochomatin also varies between cell lines in a manner inconsistent with the canonical model. In some cell lines repair rates were efficient in heterochromatin, comparable to transcription coupled repair, but in some tumour-derived and repair-deficient cell lines we have detected deficient repair.

In eukaryotic cells arrested in S-phase, checkpoint controls normally restrain mitosis until after replication. We have identified an array of previously unsuspected factors that modulate this restraint, using transformed hamster cells in which cycle controls are known to be altered in S-phase arrest. Arrested cells accumulate cyclin B, the regulatory partner of the mitotic p34(cdc2) kinase, which is normally not abundant until late G(2) phase; treatment of arrested cells with caffeine produces rapid S-phase condensation. We show here that such S-phase checkpoint slippage, as visualised through caffeine-dependent S-phase condensation, correlates with rodent origin and transformed status, is opposed by reverse transformation, and is favoured by c-src and opposed by wnt1 overexpression. Slippage is also dependent on a prolonged replicative arrest, and is favoured by arrest with hydroxyurea, which inhibits ribonucleotide reductase. This last is a key enzyme in deoxyribonucleotide synthesis, recently identified as a determinant of malignancy. Addition of deoxyribonucleosides shows that rapid S-phase condensation is suppressed by a novel checkpoint mechanism: purine (but not pyrimidine) deoxyribonucleosides, like reverse transformation, suppress cyclin B/p34(cdc2) activation by caffeine, but not cyclin B accumulation. Thus, ribonucleotide reductase has an unexpectedly complex role in mammalian cell cycle regulation: not only is it regulated in response to cycle progression, but its products can also reciprocally influence cell cycle control kinase activation.

Using a positive selection system for isolating DNA replication and repair related mutants, we isolated a clone from a rat kangaroo cell line (PtK2) that has increased sensitivity to UV light. Characterization of this clone indicated normal post-replication repair after UV irradiation, and normal removal rates of cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts by excision repair. However, this cell line has decreased ability to make early incisions on damaged DNA, possibly indicating a defect in preferential repair of actively transcribed genes, and a slower cell proliferation rate, including a longer S-phase. This phenotype reinforces the present notion that control of key mechanisms in cell metabolism, such as cell cycle control, repair, transcription and cell death, can be linked.

When DNA topoisomerase II (topo II) activity is inhibited with a non-DNA-damaging topo II inhibitor (ICRF-193), mammalian cells become checkpoint arrested in G2-phase. In this study, we analyzed chromosome structure in cells that bypassed this checkpoint. We observed a novel type of chromosome aberration, which we call Ω-figures. These are entangled chromosome regions that indicate the persistence of catenations between nonhomologous sequences. The number of Ω- figures per cell increased sharply as cells evaded the transient block imposed by the topo II-dependent checkpoint, and the presence of caffeine (a checkpoint-evading agent) potentiated this increase. Thus, the removal of nonreplicative catenations, a process that promotes chromosome individualization in G2, may be monitored by the topo II-dependent checkpoint in mammals.

Satellite DNAs are present on every chromosome in the cell and are typically enriched in repetitive, heterochromatic parts of the human genome. Sex chromosomes represent a unique genomic and epigenetic context. In this review, we first report what is known about satellite DNA biology on human X and Y chromosomes, including repeat content and organization, as well as satellite variation in typical euploid individuals. Then, we review sex chromosome aneuploidies that are among the most common types of aneuploidies in the general population, and are better tolerated than autosomal aneuploidies. This is demonstrated also by the fact that aging is associated with the loss of the X, and especially the Y chromosome. In addition, supernumerary sex chromosomes enable us to study general processes in a cell, such as analyzing heterochromatin dosage (i.e. additional Barr bodies and long heterochromatin arrays on Yq) and their downstream consequences. Finally, genomic and epigenetic organization and regulation of satellite DNA could influence chromosome stability and lead to aneuploidy. In this review, we argue that the complete annotation of satellite DNA on sex chromosomes in human, and especially in centromeric regions, will aid in explaining the prevalence and the consequences of sex chromosome aneuploidies.

The critical cellular defect(s) and basis for cell killing by ionizing radiation in ataxia–telangiectasia (A-T) are unknown. We use the topoisomerase I inhibitor camptothecin (CPT), which kills mainly S-phase cells and induces DSBs predominantly in replication forks, to show that A-T cells are defective in the repair of this particular subclass of DSBs. CPT-treated A-T cells reaching G2 have abnormally high levels of chromatid exchanges (viewed as prematurely condensed G2 chromosomes); aberrations in normal cells are mostly chromatid breaks. Transfectants of A-T cells with the wild-type ATM cDNA are corrected for CPT sensitivity, chromatid aberrations, and the DSB repair defect. These data suggest that in normal cells ATM, the A-T protein, probably recognizes DSBs in active replicons and targets the repair machinery to the breaks; in addition, the ATM protein is involved in the suppression of low-fidelity, adventitious rejoining between replication-associated DSBs. The loss of ATM functions therefore leads to genome destabilization, sensitivity to DSB-inducing agents and to the cancer-promoting illegitimate exchange events that follow.

The NIGMS Human Genetic Cell Repository has assembled regional mapping panels for human chromosomes 1, 2, and 7 from human rodent somatic cell hybrids submitted to the collection by researchers from 14 different laboratories. All hybrids were characterized initially by the submitters and verified by the Repository. Each hybrid carries a stable defined human segment as a derivative or deletion chromosome. These panels define 8–10 intervals for each chromosome. The panel for chromosome 2 is a new resource. The panels for chromosomes 1 and 7 complement previously published panels. The Repository distributes these regional mapping panels as cell cultures or as DNA. Information about these panels as well as for panels for chromosomes 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, and X may be viewed in the NIGMS Repository electronic catalog (http://locus.umdnj.edu/ptnigms).

Condensed sister chromatids possess a protein scaffold or axial core to which loops of chromatin are attached. The sister cores are believed to be dynamic frameworks that function in the organization and condensation of chromatids. Chromosome structural proteins are implicated in the establishment of sister chromatid cohesion and in the maintenance of epigenetic phenomena. Both processes of templating are tightly linked to DNA replication itself. It is a question whether the structural basis of sister chromatid cores is templated during S phase. As cells proceed through the cell cycle, chromatid cores undergo changes in their protein composition. Cytologically, cores are first visualized at the start of prometaphase. Still, core assembly can be induced in G1 and G2 when interphase cells are fused with mitotic cells. In this study, we asked if chromatid cores are similarly able to assemble in S-phase cells. We find that the ability to assemble cores is transiently lost during local replication, then regained in chromosome regions shortly after they have been replicated. We propose that core templating occurs coincident with DNA replication and that the competence for the assembly of the sister chromatid cores is acquired shortly after passage of replication forks.

The NIGMS Human Genetic Cell Repository has assembled regional mapping panels for human chromosomes 1, 2, and 7 from human rodent somatic cell hybrids submitted to the collection by researchers from 14 different laboratories. All hybrids were characterized initially by the submitters and verified by the Repository. Each hybrid carries a stable defined human segment as a derivative or deletion chromosome. These panels define 8-10 intervals for each chromosome. The panel for chromosome 2 is a new resource. The panels for chromosomes 1 and 7 complement previously published panels. The Repository distributes these regional mapping panels as cell cultures or as DNA. Information about these panels as well as for panels for chromosomes 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 22, and X may be viewed in the NIGMS Repository electronic catalog (http://locus.umdnj.edu/nigms).