Localization of Drosophila nasutoides satellite DNAs in metaphase chromosomes

Metaphase chromosomes of D. nasutoides were hybridized situ with ³H-cRNA synthesized from the four satellites which make up 50–60% of the total DNA of this species. All four satellites were localized in the large, metacentric, heterochromatic chromosome four. They did not, however, appear to hybridize to centromeric or other constitutive heterochromatin, nor did they, with the exception of satellite I, seem to hybridize in the specific regions of chromosome four which, on the basis of C, Q, and H banding and AT contents, were predicted to contain some of these satellites. —Comparison of grain patterns with the results of fluorescent staining indicated that satellite-bearing heterochromatin was not always associated with other fractions of constitutive heterochromatin in interphase nuclei and was, at least partially, decondensed in some larger nuclei.     

Early S phase DNA replication: A search for targets of carcinogenesis

Our studies have revealed that replicating DNA is more vulnerable to adduction than is non-replicating DNA. Contrary to our expectations that the vulnerability to neoplastic transformation induced by carcinogens in synchronized cells would parallel the rate of DNA replication, we actually found that the vulnerability was notably increased early in the S phase and more closely paralleled the rate of entry of cells into the S phase (the very beginning of S phase) rather than the overall rate of DNA synthesis. From these findings we hypothesized that there were targets for the neoplastic transformation of cells that were among the earliest replicated sequences in the genome. To test that this hypothesis was plausible we investigated the temporal order of DNA replication during the S phase and showed that the order of DNA replication was far more precisely defined than had been recognized previously. The cell synchronization techniques that made those findings possible made it feasible to demonstrate that only a relatively few sites of DNA replication are identifiable in chromosomal bands at the earliest times in the S phase. The same synchronization techniques enabled us to label DNA replicated when populations of cells were very early in S phase and to isolate and clone this DNA. The clonal elements of this library of DNA prepared in this manner have been sequenced and mapped to the human genome. Efforts are in progress to characterize the genes and sequence features associated with these regions. We have utilized methods to identify and characterize origins of DNA replication as a means of locating the earliest replicating part of these early replicating regions. We have identified several new origins of DNA replication that are activated early and late in the S phase but the features of the chromatin at the origin that determines its time of activation remain obscure. In an effort to improve our ability to identify more origins, particularly adjacent origins in genomic regions, we have combined the methods of DNA combing and FISH analysis of combed DNA to search for DNA precursor incorporation patterns characteristic of origins of DNA replication. Preliminary nascent strand abundance studies appear to have proven the existence of two origins of DNA replication predicted from the precursor incorporation studies. We have found that the combed DNA techniques can be combined with precursor incorporation studies and antibodies to sites of DNA damage to address questions of mechanisms of DNA damage and repair. For example these studies have shown recently that DNA damage is not randomly distributed in the genome and that both inhibition of replicon initiation and inhibition of strand elongation are separately distinguishable as components of the S checkpoint function.It is our hope and expectation that these results and the opportunities that they provide for future studies will enable us to identify possible targets for malignant transformation that explain our observation that cells at the start of S phase are vulnerable to the initiation of carcinogenesis.     

Is activation of the intra-S checkpoint in human fibroblasts an important factor in protection against UV-induced mutagenesis?

The ATR/CHK1-dependent intra-S checkpoint inhibits replicon initiation and replication fork progression in response to DNA damage caused by UV (UV) radiation. It has been proposed that this signaling cascade protects against UV-induced mutations by reducing the probability that damaged DNA will be replicated before it can be repaired. Normal human fibroblasts (NHF) were depleted of ATR or CHK1, or treated with the CHK1 kinase inhibitor TCS2312, and the UV-induced mutation frequency at the HPRT locus was measured. Despite clear evidence of S-phase checkpoint abrogation, neither ATR/CHK1 depletion nor CHK1 inhibition caused an increase in the UV-induced HPRT mutation frequency. These results question the premise that the UV-induced intra-S checkpoint plays a prominent role in protecting against UV-induced mutagenesis.     

DNA repair and replication in human fibroblasts treated with (±)-r-7,t-8-dihydroxy-t-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene

DNA repair and replication were examined in diploid human fibroblasts after treatment with (±)-r-7,t-8-dihydroxy-t-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE-I). Unscheduled DNA synthesis exhibited a linear response to BPDE-I concentrations up to 1.5 μM and a saturation plateau after higher concentrations. Maximal unscheduled DNA synthesis was observed in the first hour after treatment with synthesis diminishing progressively thereafter. Half-maximal unscheduled DNA synthesis was seen within 4–6 h after treatment with 0.7 μM BPDE-I. DNA replication was inhibited by BPDE-I in a dose- and time-dependent fashion. The mechanisms of this inhibition were characterized by velocity sedimentation of pulse-labeled nascent DNA in alkaline sucrose gradients. Very low concentrations of BPDE-I (0.03 and 0.07 μM) were found to inhibit replicon initiation by up to 50% within 30–60 min after treatment. Recovery of initiation following these low concentrations was evident within 3 h after treatment. Higher concentrations of carcinogen inhibited DNA synthesis in active replicons. This effect was manifested by a reduction in incorporation of precursor into replication intermediates of greater than 1·10⁷ Da with the concurrent production of abnormally small nascent DNA. When viewed 45 min after treatment with 0.17 μM BPDE-I the combination of these two effects partially masked the inhibition of replicon initiation. However, even after treatment with 0.33 μM BPDE-I an effect on initiation was evident. These results reveal a pattern of response to BPDE-I that is quite similar to that produced by 254 nm radiation.     

Adenovirus mediated transduction of the human DNA polymerase eta cDNA

Xeroderma pigmentosum (XP) is an autosomal recessive photosensitive disorder with an extremely high incidence of skin cancers. Seven complementation groups, corresponding to seven proteins involved in nucleotide excision repair (NER), are associated with this syndrome. However, in XP variant patients, the disorder is caused by defects in DNA polymerase eta; this error prone polymerase, encoded by POLH, is involved in translesion DNA synthesis (TLS) on DNA templates damaged by ultraviolet light (UV). We constructed a recombinant adenovirus carrying the human POLH cDNA linked to the EGFP reporter gene (AdXPV-EGFP) and infected skin fibroblasts from both XPV and XPA patients. Twenty-four hours after infection, the DNA polymerase eta-EGFP fusion protein was detected by Western blot analysis, demonstrating successful transduction by the adenoviral vector. Protein expression was accompanied by reduction in the high sensitivity of XPV cells to UV, as determined by cell survival and apoptosis-induction assays. Moreover, the pronounced UV-induced inhibition of DNA synthesis in XPV cells and their arrest in S phase were attenuated in AdXPV-EGFP infected cells, confirming that the transduced polymerase was functional. However, over-expression of polymerase eta mediated by AdXPV-EGFP infection did not result in enhancement of cell survival, prevention of apoptosis, or higher rate of nascent DNA strand growth in irradiated XPA cells. These results suggest that TLS by DNA polymerase eta is not a limiting factor for recovery from cellular responses induced by UV in excision-repair deficient fibroblasts.     

An ATR- and Chk1-dependent S checkpoint inhibits replicon initiation following UVC-induced DNA damage

Inhibition of replicon initiation is a stereotypic DNA damage response mediated through S checkpoint mechanisms not yet fully understood. Studies were undertaken to elucidate the function of checkpoint proteins in the inhibition of replicon initiation following irradiation with 254 nm UV light (UVC) of diploid human fibroblasts immortalized by the ectopic expression of telomerase. Velocity sedimentation analysis of nascent DNA molecules revealed a 50% inhibition of replicon initiation when normal human fibroblasts were treated with a low dose of UVC (1 J/m(2)). Ataxia telangiectasia (AT), Nijmegen breakage syndrome (NBS), and AT-like disorder fibroblasts, which lack an S checkpoint response when exposed to ionizing radiation, responded normally when exposed to UVC and inhibited replicon initiation. Pretreatment of normal and AT fibroblasts with caffeine or UCN-01, inhibitors of ATR (AT mutated and Rad3 related) and Chk1, respectively, abolished the S checkpoint response to UVC. Moreover, overexpression of kinase-inactive ATR in U2OS cells severely attenuated UVC-induced Chk1 phosphorylation and reversed the UVC-induced inhibition of replicon initiation, as did overexpression of kinase-inactive Chk1. Taken together, these data suggest that the UVC-induced S checkpoint response of inhibition of replicon initiation is mediated by ATR signaling through Chk-1 and is independent of ATM, Nbs1, and Mre11.     

Ubiquitylation of proliferating cell nuclear antigen and recruitment of human DNA polymerase eta

This study investigated the requirement for ubiquitylation of PCNA at lysine 164 during polymerase eta-dependent translesion synthesis (TLS) of site-specific cis-syn cyclobutane thymine dimers (T (wedge)T). The in vitro assay recapitulated origin-dependent initiation, fork assembly, and semiconservative, bidirectional replication of double-stranded circular DNA substrates. A phosphocellulose column was used to fractionate HeLa cell extracts into two fractions; flow-through column fraction I (CFI) contained endogenous PCNA, RPA, ubiquitin-activating enzyme E1, and ubiquitin conjugase Rad6, and eluted column fraction II (CFII) included pol delta, pol eta, and RFC. CFII supplemented with purified recombinant RPA and PCNA (wild type or K164R, in which lysine was replaced with arginine) was competent for DNA replication and TLS. K164R-PCNA complemented CFII for these activities to the same extent and efficiency as wild-type PCNA. CFII mixed with CFI (endogenous PCNA, E1, Rad6) exhibited enhanced DNA replication activity, but the same TLS efficiency determined with the purified proteins. These results demonstrate that PCNA ubiquitylation at K164 of PCNA is not required in vitro for pol eta to gain access to replication complexes at forks stalled by T (wedge)T and to catalyze TLS across this dimer.