The evolution of base sequences in polynucleotides

Biological aspects of cytosine methylation in eukaryotic cells

The existence in eukaryotes of a fifth base, 5-methylcytosine, and of tissue-specific methylation patterns have been known for many years, but except for a general association with inactive genes and chromatin the exact function of this DNA modification has remained elusive. The different hypotheses regarding the role of DNA methylation in regulation of gene expression, chromatin structure, development, and diseases, including cancer are summarized, and the experimental evidence for them is discussed. Structural and functional properties of the eukaryotic DNA cytosine methyltransferase are also reviewed.

In vivo studies on DNA repair and turnover with age

Since the capacity for DNA repair relative to other cellular processes should be an important parameter of mutagenesis, carcinogenesis, and also aging, this capacity should preferably be studied in intact animals. Thus, we developed autoradiographic techniques for measuring DNA repair directly in vivo. By these methods unscheduled DNA synthesis (UDS) was detected quantitatively as silver grains on epithelial cells of mouse skin after treatment with chemical carcinogens or UV irradiation, and on cerebral ganglion cells of aquarium fish after treatment with various chemical carcinogens. Several interesting findings so far obtained are presented. Possible age-related change in the UDS response was examined by the skin technique with mice of 2 and 18 months old. Similar dose-dependent induction of UDS was observed in mice of both ages after treatment with 4-hydroxyaminoquinoline 1-oxide; their levels of UDS at each dose were not significantly different. The dose-response curves for young and aged animals after UV irradiation showed similar increases to a plateau at low doses, but their responses to high doses were very different: in aged mice the UDS level decreased markedly with increase in the dose, whereas in young mice it remained at the same level. This suggests that in aged animals, high doses of UV irradiation cause deterioration of DNA repair systems, and that aged animals cannot repair extensive DNA damage efficiently. It is generally thought that DNA has a stable structure and a much slower turnover than other cellular components. Although the effect of DNA repair on DNA turnover may be insignificant, accumulation of repaired DNA in cells should result in detectable DNA turnover. Therefore, we investigated DNA turnover in postmitotic ganglion cells of rat retina. However, careful autoradiographic studies on pairs of eyes showed no detectable DNA turnover up to nearly their median life span (2 years). This result suggests that the DNA of post-mitotic cells, which are not replaced throughout the life span of the animal, is very stable and is possibly protected in some special way.

Changes in the quantity of histone and actin messenger RNA during the development of preimplantation mouse embryos

Actin and histone H3 mRNA levels in mouse eggs and early embryos have been measured by use of recombinant DNA probes having sequence homology to those mRNA species. Total nucleic acid was extracted from pools of unfertilized eggs, two-cell embryos, eight-cell embryos, and blastocysts. The nucleic acids were resolved electrophoretically, bound to diazotized paper following Northern transfer, and hybridized with 32P-labeled histone or actin DNA probes. Our findings demonstrate that there is a maternal store of histone and actin mRNA in the unfertilized egg but that this mRNA pool is reduced roughly 10-fold on an embryo basis by the mid-two-cell stage. Following this reduction of maternal mRNA, histone and actin mRNA accumulation from the eight-cell cleavage stage to the blastocyst increases proportionally to cell number and appears to be controlled by zygote genome transcription.

Transcription and hybridization of 125I-cRNA from flow sorted chromosomes

Metaphase chromosomes from the Chinese hamster cell line M3-1 were separated by means of a flow sorter. Two chromosome fractions were used for this study: A, which consisted of 95% pure chromosome no. 1, and B, which was 90% pure chromosome no. 2. The DNA of 10(6) chromosomes of each type was purified, and a 125I-cRNA transcript was synthesized in a reaction containing E. coli RNA polymerase and carrier-free 125I-CTP (1.7 Ci/mumole). The cRNA product synthesized with template DNA from 10(5) sorted chromosomes contained more than 10(6) dpm. The electrophoretic mobility profiles of the cRNAs on 7.5% SDS acrylamide gels demonstrated that more than 50% of the ribo-polymers were equal to or longer than marker E. coli met-tRNAf. In hybridization reactions 21% and 17% of the transcripts from Chinese hamster whole cell and sorted chromosome DNA hybridized to Chinese hamster DNA and did not hybridize significantly over background in reactions containing calf DNA at Crt values of 1.3 and 1.9 x 10(2) mole sec/l. Labelled cRNAs transcribed from the DNA of sorted chromosomes hybridized with the DNA of each sorted chromosome fractions at a Crt of 0.6 mole sec/l. This study demonstrated that the DNA can be (1) recovered from small numbers of highly purified flow sorted chromosomes, (2) used as template by E. coli RNA polymerase and (3) used to prepare a cRNA in reactions containing polymerase and carrier-free 125I-CTP to yield a product which can be employed for hybridization analysis.

RNA processing and RNA tumor virus origin and evolution

The results of molecular hybridization experiments with high-molecular-weight RNA isolated from RNA tumor viruses and DNA from normal cells suggest that RNA tumor virus genomes originate from cell genes. Some RNA tumor viruses (here called class 1) appear to have been generated in recent times in that their RNA is closely related in nucleotide sequence to certain cell genes (class 1 genes). A second class of RNA tumor viruses (here called class 2) is more distantly related to genomic information of normal cells. Structural properties of the RNA of RNA tumor viruses lead us to propose that the tumor virus RNA is originated when RNA transcripts of class 1 genes are processed by a mechanism we call "paraprocessing." We postulate that RNA paraprocessing is normally used only at particular times during differentiation and is characterized by the cytoplasmic appearance of high-molecular-weight RNA chains containing terminal polyadenylic acid (200 residues). Paraprocessing of class 1 gene transcripts in committed or differentiated cells is considered to be aberrant in transcription that can lead to the generation of an RNA tumor virus genome. If the paraprocessed class 1 gene transcript codes for a reverse transcriptase, replication of the RNA becomes possible. Transfer of the replicating RNA to a new cell can result in genetic change such that the virus genome mutates, differing from the original progenitor genes. We propose that this genetic change causes class 1 viruses to become class 2. These ideas are applied to evidence concerning the biology of infection of RNA tumor viruses and concerning the involvement of RNA tumor viruses in human cancer. Genetic change can also occur during the origination of an RNA tumor virus genome by repeated reverse transcription and recombination (45) or by genetic alteration of particularly changeable cell genes ("hot spots") (43).

Reconstitution of chromatin: mode of reassociation of chromosomal proteins

The mode of reassociation of Ehrlich ascites histones and non-histone proteins during chromatin reconstitution was studied by sodium dodecyl sulfate polyacryl-amide gel electrophoresis. In the procedure of Bekhor et al. (I. Bekhor, G. M. Kung, and J. Bonner, (1969), J. Mol. Biol. 39, 351) most of histones and non-histone proteins reassociate with DNA in the last dialysis step of the dissociated chromatin, that is the dialysis of the chromatin in 0.4 M NaCl-5 M urea against a dilute buffer. The reassociation of histones and non-histone proteins with DNA is more gradual in the procedure of L. Kleiman and R.-C. C. Huang [(1972), J. Mol. Biol. 64, 1]. However, in both procedures the bulk of the Ehrlich ascites non-histone proteins reassociate with DNA after the binding of histones to DNA. There are small amounts of non-histone proteins which reassociate with DNA before and at the same time as histones reassociate with DNA.

DNA base composition of some free-living nematode species

The mean base compositions (% GC) of DNA samples from five free-living nematodes were determined by CsCl equilibrium buoyant-density centrifugation and thermal denaturation studies. Both methods gave similar results indicating that there is no extensive replacement of the usual bases in nematode DNA. From the ultracentrifugation studies the % GC content of the DNA of Caenorhabditis briggsae (Dougherty and Nigon, 1949) Dougherty, 1953, Turbatrix aceti (Müller, 1783) Peters, 1927, Rhabditis (Rhabditis) anomala Hertwig, 1922 (Dougherty 1955), Panagrellus redivivus (Linn, 1767) T. Goodey, 1945, and Panagrellus silusiae (de Man, 1913) T. Goodey, 1945 was 36, 40, 42, 44 and 44, respectively.The sample of DNA from T. aceti showed two distinct ultraviolet absorbing bands in a CsCl gradient. The band at 1.688 g/cm3 proved to be a polysaccharide. It gave a distinctive refractive index pattern when viewed with the schlieren optical system, was insensitive to DNase treatment and was removed by a-amylase treatment. On the other hand, the material banding at 1.699 g/cm3 was shown to be DNA. This band produced no disturbance in the refractive index gradient. It was not altered by a-amylase treatment, but it was DNase sensitive.Since P. redivivus and P. silusiae were found to have the same DNA base composition their ability to interbreed was examined. These two forms were cross-fertile and the offspring were fully fertile.

The cytoplasmic RNA of HeLa cells: new discrete species associated with mitochondria

Two new species of cytoplasmic RNA with approximate sedimentation values of 12S and 21S, and which appear associated with mitochondria, are described. The species are unmethylated, are relatively metabolically stable, and have a 43 per cent G + C content. Their synthesis is uniquely resistant to inhibition by UV irradiation. The 12S and 21S RNA do not appear to be components of polysome-like structures.

Characteristics of the RNA synthesized in vitro by the normal human small lymphocyte and the changes induced by phytohemagglutinin stimulation

These studies demonstrate that the circulating human small lymphocyte synthesizes ribonucleic acid (RNA) of high molecular weight which is not primarily a ribosomal precursor and which is, in part, complementary to human deoxyribonucleic acid (DNA). The stimulation of these lymphocytes by PHA brings a cell population in which few ribosomes are synthesized to a functional condition in which a large amount of these particles are produced. This increase in the synthesis of ribosomal RNA is one of the earliest and most relevant effects of PHA on the RNA metabolism of small lymphocytes.