DNA chain growth in isolated HeLa nuclei

CDA directs metabolism of epigenetic nucleosides revealing a therapeutic window in cancer

Cells require nucleotides to support DNA replication and to repair damaged DNA. In addition to de novo synthesis, cells recycle nucleotides from the DNA of dying cells or from cellular material ingested through the diet. Salvaged nucleosides come with the complication that they can contain epigenetic modifications. Since epigenetic inheritance of DNA methylation mainly relies on copying of the modification pattern from parental strands^1-3, random incorporation of pre-modified bases during replication could have profound implications for epigenome fidelity and yield adverse cellular phenotypes. Although the salvage mechanism of 5-methyl-2′deoxycytidine (5mdC) has been investigated before^4-6, currently it remains unknown how cells deal with the recently identified oxidised forms of 5mdC – 5-hydroxymethyl-2′deoxycytidine (5hmdC), 5-formy-2′deoxycytidine (5fdC) and 5-carboxyl-2′deoxycytidine (5cadC)^7-10. Here we demonstrate that enzymes of the nucleotide salvage pathway display substrate selectivity, effectively protecting newly synthesized DNA from the incorporation of epigenetically modified forms of cytosine. Thus cell lines and animals can tolerate high doses of these modified cytidines without any deleterious effects on physiology. Interestingly, by screening cancer cell lines for growth defects following exposure to 5hmdC, we unexpectedly identify a subset of cell lines where 5hmdC or 5fdC administration leads to cell lethality. Using genomic approaches we discover that the susceptible cell lines overexpress cytidine deaminase (CDA). CDA converts 5hmdC and 5fdC into variants of uridine that are incorporated into DNA, resulting in accumulation of DNA damage and ultimately, cell death. Our observations extend current knowledge of the nucleotide salvage pathway by revealing the metabolism of oxidised epigenetic bases, and suggest a therapeutic option for cancers, such as pancreatic cancer, that have CDA overexpression and are resistant to treatment with other cytidine analogues¹¹.

DNA methylation in mammalian nuclei

A novel system to study the methylation of newly synthesized DNA in isolated nuclei was developed. Approximately 2.5% of cytosine residues incorporated into nascent DNA became methylated by endogenous methylase(s), and the level of DNA modification was reduced by methylation inhibitors. DNA synthesis and methylation were dependent on separate cytosol factors. The cytosol factor or factors required for DNA methylation were sensitive to trypsin digestion and were precipitable by (NH4)2SO4, suggesting that they were proteinaceous. Time-course experiments revealed a short lag of approximately 20 s between synthesis and methylation in nuclei. The DNAs produced in these nuclei were a mixed population of low molecular weight fragments and higher molecular weight fragments shown to be short extension of existing replicons. The methylation level found in low molecular weight DNA was lower than that found in bulk L1210 DNA, indicating that further methylation events might take place after ligation of small fragments. These data suggest that newly synthesized DNA is a good substrate for methylase enzymes and that nuclear cytoplasmic interactions may be important in controlling inheritance of methylation patterns.

Role of cytosol proteins in DNA chain growth and chromatin replication in Friend erythroleukemia cell nuclei

The influence of cytosol proteins on the replication of DNA and chromatin in isolated nuclei from Friend erythroleukemia cells has been investigated. The overall process has been clearly shown to proceed stepwise. In the absence of cytosol proteins DNA chain growth tends to stop after the addition of approximately 200 nucleotides to the ends of growing chains. In the presence of cytosol proteins these sections grow to approximately 250 nucleotides, and participate in the stepwise extension of the replication process through adjacent nucleosomal sections of the template. Immediately following pulse labeling, the newly replicated DNA resides in a chromatin form which appears to be relatively resistant to digestion by micrococcal nuclease. During a chase interval, the association of the pulse-labeled DNA with nuclear proteins matures to a form which yields lengths of DNA upon digestion with micrococcal nuclease that correspond to mono-, di-, tri- and polynucleosomal units of chromatin. In the absence of cytosol proteins the nuclease resistant state of the labeled DNA tends to predominate and persist. The data support the view that DNA replication in a chromosomal setting proceeds stepwise over successive nucleosomal sections of template made accessible by the interaction of the cytosol proteins at or near the replication fork.

DNA synthesis in isolated chromatin. Nature of activities, and relationship to kinetics of DNA polymerase release from chromatin DNA

Chromatin isolated from Ehrlich ascites tumor cells showed two DNA synthetic activities differing in sensitivity to N-ethylmaleimide. For studies on the nature of activities and relationship to kinetics of DNA polymerase, a new method was developed for detecting the activity of DNA polymerase released from chromatin DNA during DNA synthesis in vitro. The activity of DNA polymerase released was measured in a reaction mixture for DNA synthesis using exogenously added poly(dA-dT) as a template-primer in the presence of actinomycin D. Evidence that the DNA polymerase released was actually involved in DNA synthesis of chromatin was obtained in experiments using chromatin isolated from cells treated with various concentrations of 1-beta-D-arabinofuranosylcytosine and chromatin from adult mouse liver. The experiments showed that chromatin isolated from cells in which only small amount of DNA polymerase was engaged in DNA synthesis released a negligible amount of DNA polymerase, especially N-ethylmaleimide-sensitive polymerase. Kinetic analysis of DNA polymerase during chromatin DNA synthesis by the new method suggested that KCl at the optimal concentration (10-20 mM) for the N-ethylmaleimide-sensitive chromatin activity enhanced the binding of the N-ethylmaleimide-sensitive DNA polymerase to chromatin DNA. From the findings that addition of actinomycin D or omission of dNTPs from the preincubation mixture prevents this binding, it is suggested that the binding of DNA polymerase is followed by the DNA chain synthesis and that the DNA polymerase involved in this reaction is N-ethylmaleimide sensitive. Data on the effect of KCl on the rate of chromatin DNA synthesis and on the size of the DNA chain favor this assumption.

Effect of Ehrlich ascites cell chalone on nascent DNA synthesis in isolated nuclei

Ehrlich Ascites Tumor (EAT) chalone has been shown to inhibit nascent DNA synthesis by inhibiting DNA polymerase alpha and beta (Nakai, 1976), but one of the problems in studying eurkaryotic DNA replication has been the relative impermeability of the cell membrane to precursors and macromolecules; hence, to circumvent this restriction without sacrificing the integrity of the replication process, a broken cell system utilizing nuclei in aqueous media was investigated. Isolated nuclei appear to continue the process of DNA replication that was proceeding in vivo before their isolation and under optimal concitions are able to initiate new synthesis (Fraser & Huberman, 1977). The effects of partially purified EAT chalone on nascent DNA could be studied directly in this nuclear system, which excluded effects of the cell membrane, nucleotide pools and other cytosol elements. A concentration-related inhibition of [3H]thymidine triphosphate ([3H]dTTP) incorporation was noted over a chalone range of 50-200 micrograms/ml. It appears that chalone can inhibit DNA polymerase alpha directly within the nucleus without an intermediate step such as a cell membrane receptor.

Isolation of a stimulatory factor for nuclear DNA replication

Aqueous extracts of isolated nuclei and intact plasmodia of Physarum contain a heat-stable stimulator of nuclear DNA replication. The stimulatory factor is present throughout the mitotic cycle, and its activity is unaffected by prior exposure of plasmodia to cycloheximide. The stimulatory substance has been partially purified by heat treatment, precipitation with ethanol, chromatography on DEAE cellulose, and gel filtration. The purified material contains both carbohydrate and protein, and exhibits a molecular weight of about 30 000. The active substance increases the rate and overall extent of DNA replication in S-phase nuclei, but does not trigger the initiation of DNA synthesis in nuclei isolated from G2-phase plasmodia. The stimulatory material contains little or no deoxyribonuclease or DNA polymerase activity, and it does not affect DNA polymerase activity assayed using a purified DNA template.