Changes in the methylated sequences and molecular population of wheat DNA during germination

The fractions of unique (Cot less than 405), moderately (Cot=0.13--405) and highly reiterated (Cot less than 0--0.13) sequences were isolated from DNA of wheat seeds and 3 day old seedlings, and GC content, amount of 5-methylcytosine and its distribution among various pyrimidine isostichs in the fractions isolated were studied. Different in Cot value DNA fractions from seeds or from seedlings are similar in GC content and in all other characteristics studied. Seed DNA differs from DNA of seedlings in the content of pyrimidine isostichs from the respective fractions of reiterated sequences. Pronounced differences in the amount of pyridmidine clusters with various base composition in the corresponding fractions of DNA from seeds and seedlings were found. These differences in the frequencies of respective pyrimidine clusters from DNA of seeds and seedlings may be considered as being a result of changes in the molecular population of wheat DNA on germination. The seed and seedling DNA differ significantly in the 5-methylcytosine content in the respective pyrimidine isostichs isolated from unique sequences. In the seedling DNA some other nucleotide sequences are to be methylated as compared to DNA of dormat seeds. Thus, on germination some changes occur in DNA methylation as well as in the genome organization.     

Changes in base composition and molecular population of wheat DNA on germination]

Germination of wheat seeds results in small changes of the GC content of total DNA (from 47.5 to 49.0 mole %): at the same time the amount of 5-methylcytosine in seeds 10 hours after wetting and at day 3 of germination significantly decrease (from 6.0 to 5.4 and 5.2 mole %, respectively). The wheat genome is methylated in non-uniform fashion: moderute repeats (less than a hundred copies, interval Cot = 0,12 . 10(2)-420) possess the maximal amount of 5-methylcytosine, while the unique sequences (Cot greater than 420) have the lowest 5-methylcytosine content. Methylation of highly reiterated sequences (Cot less than 0,8 . 10(-2) is similar to that of the total DNA. At day 3 of germination the amount of 5-methycytosine in all DNA fractions is lower as compared with these fractions isolated from DNA of dormant seeds. This is probably due to (1) diminution in the amount of reiterated sequences with high 5-methylcytosine content and (2) to lowering of DNA methylation level in germinating seeds. Changes in DNA methylation may be associated with the regulation of gene activity in the differentiating plant cells at various stages of ontogenesis.     

Effect of in vitro shoot multiplication and somatic embryogenesis on 5-methylcytosine content in DNA of Myrtus communis L.

Reversed-phase HPLC analysis of 2-deoxynucleosides was performedto study the amount of 5-methylcytosine in genornic DNA of Myrtuscommunis L. About 11% cytosines were found to be methylated inDNA of field growing shoots. This amount showed no variation after theestablishment of shoots in vitro or their subsequentrooting and acclimatisation to ex vitro conditions.Therefore, adult elite plants can be micropropagated and transferred to thefield without global DNA methylation changes. Likewise, no trend in5-methylcytosine content was introduced by increasing the number of subculturesin either adult- or seedling-originated shoot stocks. On the other hand, nodifference was found in DNA methylation after plant regeneration fromembryogenic calli. The significance of a tissue culture model system with noglobal hypo- or hypermethylation is discussed.     

A high amount of satellite DNA in the genome of Lupinus angustifolius L.

Embryo DNA, isolated from ungerminated seeds of Lupinus angustifolius L., contains an exceptionally high amount of guanine-cytosine-rich satellite DNA. The thermal denaturation curve of total embryo DNA is biphasic with an inflexion point at 62% denaturation, indicating the presence of satellite DNA. The satellite fraction could be separated from the mainband DNA by three successive preparative CsCl-gradient centrifugations. The densities of the DNA fractions are 1.7045 g cm^-3 and 1.6925 g cm^-3, respectively. The percentages of guanine-cytosine calculated from these densities are comparable to the percentages of GC calculated from the melting temperatures. Finally, ressociation studies prove that foldback DNA and highly repeated sequences are much more frequent in the satellite DNA fraction than in the mainband DNA.Abbreviation C _o t the product of the DNA concentration (mol nucleotides l^-1) and the time (s) of incubation in a DNA reassociation reaction - GC guanine-cytosine - np nucleotide parirs - T temperature interval between 16 and 84% denaturation     

The structure of animal mitochondrial DNA (base composition,pyrimidine clusters,character of methylation)

Summary Base composition, content of pyrimidine isopliths and the degree of methylation of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) from various vertebrates and protozoonCrithidia oncopelti have been studied. MtDNAs from mammals (ox, rat) do not differ in fact in the GC content from the respective nDNA. The GC content in mtDNA from fishes (sheat fish) and birds (duck, chicken) is 1.5–2.5 mole % higher than in the respective nDNA. Kinetoplast DNA (kDNA) fromCrithidia oncopelti (GC = 42.9 mole %) differs significantly in base composition from nDNA (GC = 51.3 mole %). All the mtDNA and kDNA studied differ from the respective nDNA by a lower degree of pyrimidine clustering. Th amount of mono and dipyrimidine fragments in mtDNA is more than 30 mole %, whereas in nDNA it does not exceed 23 mole %. The quantity of long pyrimidine clusters (hexa and others) is 2–4 times lower in mtDNA than in nDNA. The lower degree of clustering of pyrimidine nucleotides seems to be a specific feature of all the mtDNA studied. This may be indicative of common traits in the organization and origin of mtDNA. All mtDNA of vertebrates contain 5-methylcytosine as a minor base (1.5–3.15 mole %) and surpass by 1.5–2 times the respective nDNA in the methylation degree. It has been found that in animals mtDNA is species specific as far as the 5-methyl-cytosine content is concerned. In mitochondria and nuclei of rat liver certain DNA methylase activity has been detected, which providesin vitro the methylation of cytosine residues both in homologous DNA and various heterologous DNAs. The specificity of methylationin vitro of cytosine residues in the same heterologous DNA fromE. coli B varies with the source of enzymes. The mitochondrial enzyme methylates cytosine as the lone monopyrimidine residue, whereas the nuclear enzyme methylates cytosine in the di- and tripyrimidine fragments.     

Reciprocal induction of cell division by cells of complementary mating types in Tetrahymena

Chick embryo fibroblasts in monolayer culture were synchronized by contact inhibition and serum starvation. Nuclear DNA isolated from the [³H] thymidine pulse-labelled cells throughout the period of DNA synthesis (S phase) was analysed by hydroxylapatite chromatography after renaturation at different C₀t values. It is shown that repeated sequences having different frequencies of reassociation, replicate differently throughout the S period. In order to study the distribution of the repeated sequences, DNA isolated during the S period was fractionated according to its buoyant density. It is shown that only some of the highly reiterated sequences which are included in the high buoyant density DNA fractions, replicate equally well during the early and the late S periods. By contrast, reiterated sequences of the low buoyant density DNA fractions replicate mainly during the late S period.     

Content and localisation of 5-methylcytosine in DNA of healthy and wilt-infected cotton plants.

5-Methylcytosine has been found in all pyrimidine isopliths isolated from the DNA of cotton plants, but it localizes predominantly in tri- (about 52%) and dipyrimidine (about 22%) clusters. The 5-methylcytosine distribution by pyrimidine isopliths in DNA of cotton plants is specific and quite different from that in other plant and animal DNA studied. The total 5-methylcytosine content in DNA from wilt-infected cotton plants (2.3 mol %) is less than half that found in DNA from non-infected cotton plants (4.9 mol %). No other visible differences (G+C content, Tm, deltaT, s20,w, frequencies of pyrimidine clusters and others) in these DNA have been found. This suggests that in wilt-infected plants, no essential alteration in DNA sequence or molecular population takes place. As a result of wilt infection 5-methylcytosine completely disappears from dipyrimidine oligonucleotides of cotton plant DNA; its content decreases markedly in long pyrimidine clusters (heptaoligonucleotides and longer) and in C3, C2 T, CT2 fragments. Thus, DNA in wilt-infected plant cells is specifically undermethylated (demethylated). The induced alteration in DNA methylation may be considered one of the possible mechanisms for the specific distortion of gene activity of host cells and primary fungal pathogenic action on plants.     

Lack of correlation between DNA-methylating activity and appearance of the immunogenic phenotype in clones of a murine lymphoma treated with mutagens

Summary The relationship between induction of novel immunogenicity by xenogenizing chemicals and DNA-methylating activity in murine tumors was investigated at the clonal level in L1210Ha cells treated with 5-azacytidine, N-methyl-N-nitro-N-nitrosoguanidine (MNNG) or 1-(p-chlorophenyl)-3,3-dimethyltriazene (DM-Cl). Cells were exposed to the drugs in vitro, cloned by limiting dilution, and assayed for transplantation immunogenicity and 5-methylcytosine content. The results showed that 0% (0/29, 5-azacytidine), 6.8% (2/29, MNNG) and 87.5% (28/32, DM-Cl) of the resulting clones were highly immunogenic, as judged by their tumorigenicity in intact compared to immunodepressed hosts. Frequency distribution analysis of the 5-methylcytosine content of drug-treated and parental clones showed that the methylation pattern was not significantly modified by tumor exposure to either 5-azacytidine or MNNG, and the two immunogenic clones induced by MNNG had methylcytosine levels very close to the 50th percentile value. In contrast, the extent of DNA methylation was increased in the cells treated with DM-Cl, but no obvious association was found between methylation status and immunogenicity of the drug-treated clones. In four 5-azacytidine-treated clones that displayed little or no immunogenicity, additional rounds of drug exposure led to progressive DNA demethylation, but failed, as a rule, to enhance tumor cell immunogenicity. Taken together, the present data indicate that, at least for the examined tumor, immunogenic variants are generated by mutagen treatment at high (MNNG) or very high (DM-Cl) frequencies under conditions in which hypomethylation-induced antigen amplification is unlikely.This work was supported by Progetto Finalizzato Oncologia, C. N. R, Rome-Italy, grant no. 87.01423.44 Abbreviations used: MNNG, N-methyl-N-nitro-N-nitrosoguanidine; DM-Cl, 1-(p-chlorophenyl)-3,3-dimethyltriazene; MST, difference (days) between median survival times of intact and irradiated mice injected with the same cells.     

Genome structure and divergence of nucleotide sequences in echinodermata

The arrangement of repetitive and single-copy DNA sequences has been studied in DNA of some species of Echinodermata — sea urchin, starfishes and sea-cucumber. Comparison of the reassociation kinetics of short and long DNA fragments indicates that the pattern of DNA sequence organization of all these species is similar to the so called Xenopus pattern characteristic of the genomes of most animals and plants. However, substantional variations have been found in the amount of repetitive nucleotide sequences in DNA of different species and in the length of DNA regions containing adjacent single-copy and repetitive sequences. Measurements of the size of S₁-nuclease resistant reassociated repetitive DNA sequences show a variability of ratios between long and short repetitive DNA sequences of different species. — The degree of divergence of short and long repetitive DNA sequences and single-copy DNA was studied by molecular hybridization of the sea urchin Strongylocentrotus intermedius ³H-DNA with the DNA of other species and by determination of the thermostability of the hybridized molecules so obtained. All three fractions of S. intermedius DNA contain sequences homologous to DNA of the other echinoderm species studied. The results obtained suggest that short repetitive DNA sequences are those which have been most highly conserved throughout the evolution of Echinodermata. A new hypothesis is proposed to explain the nature of the evolutionary changes in DNA sequence interspersion patterns.     

The chromosomes and DNA of Allium cepa

Giemsa C-banded idiograms that allow the identification of all chromosomes have been prepared for Allium cepa, Ornithogalum virens, and Secale cereale. An analysis of A. cepa DNA has determined that: (1) It has the lowest GC content so far reported for an angiosperm (32%). (2) It appears to have no satellite DNA detectable by CsCl or Cs₂SO₄-Ag⁺ density gradient centrifugation. (3) Aside from fold back DNA and unreactable fragments, a C₀t curve indicates that most of the DNA can be adequately described as two major middle repetitive components (Fractions I and II) and a single copy component (Fraction III). And (4) most of the repeated DNA sequences are involved in a short period interspersion pattern with single copy and other repetitive sequences. In situ hybridization of tritiated cRNAs to fold back, long repeated, and Fraction I DNA from A. cepa to squash preparations of chromosomes and nuclei from A. cepa, O. virens, and S. cereale root tips indicates: (1) Sequences complementary to fold back DNA are scattered throughout the genome of A. cepa except for telomeric heterochromatin and nucleolus organizers while they are not detectable in the genomes of O. virens or S. cereale. (2) Although long repeated sequences are scattered throughout the genome of A. cepa, they are concentrated to some extent in telomeric heterochromatin and nucleolus organizers (NOs). Sequences complementary to long repeats of A. cepa occur primarily in chromosome three of O. virens while these sequences are more common in the genome of more distantly related S. cereale. (3) Fraction I DNA is scattered throughout the genome of A. cepa while it is hardly detectable in the genomes of O. virens and S. cereale. These results are discussed in regard to the evolutionary conservation and function of repeated DNA sequences.     

The properties of oligonucleotide fragments containing the triphosphorylated 5′-termini of nuclear pre-mRNA from Ehrlich ascites carcinoma cells

Triphosphorylated 5-end fragments 50–150 nucleotides in length were isolated from nuclear pre-mRNA with the aid of a hydroxyapatite chromatography. They are enriched in U and G (28 and 26%, respectively). About 15% of the fragments isolated from poly(U)⁺RNA contain poly(U) tracks. Neither poly(A)-nor double-stranded sequences were found. Hybridization experiments in conditions of vast DNA excess demonstrated that the 5-end fragments contain a low amount of highly repetitive sequences but enriched in sequences hybridizing at C ₀ t 1/2 ~100.     

EcoR II is an Unreliable Enzyme for Studies of CpNpG Methylation in shape Arabidopsis thaliana

Methylation patterns from cold-inducible and embryo-specific Arabidopsis thaliana gene promoter regions were investigated. Pairs of restriction enzymes sensitive and insensitive to methylation in the same recognition sequence were used to digest genomic DNA, and the methylation status was visualized by Southern hybridization. The pair BstN I/ EcoR II should detect CpNpG methylation due to the sensitivity of EcoR II to 5-methylcytosine in the second position in the recognition sequence (5-CC(A/T)GG-3). The pair Msp I/Hpa II will detect both CpNpG methylation and CpG methylation, since Msp I does not digest the recognition sequence (5-CCGG-3) when the first C residue is methylated, while Hpa II restriction is inhibited by methylation of either of the two C residues. EcoR II digestion studies suggested CpNpG methylation in all genes tested and demethylation after cold stress in all genes (including two control embryo-specific Lea genes not induced by low temperature). Control experiments indicated an unexpected pattern of methylation and low temperature demethylation in chloroplast genes. Additional control experiments, using the methylation sensitive enzyme, ScrF I (recognizing the sequence 5-CCNGG-3), disproved the presence of 5-methylcytosine in common sites not digested by EcoR II. (CpNpG-methylation was revealed in one ScrF I site in one gene and in Msp I/Hpa II sites in two genes. CpG methylation was not found in any gene tested.) Our study indicates that results obtained using EcoR II for DNA methylation studies should be interpreted with caution. The peculiarities of the EcoR II enzyme are further discussed.     

The host specificity system inEscherichia coli SK

E. coli SK has its own enzyme system providing DNA host specificity which differs from the known types of specificity inE. coli K12 andE. coli B. Modification and restriction are observed when the PBVI or PBV3 phages are transferred fromE. coli SK toE. coli B or K12 (and back).A methylase has been isolated fromE. coli SK cells and partly purified. This methylase catalyzesin vitro transfer of the labelled methyl groups from S-adenosylmethionine (SAM) to DNA of both phage and tissue origin which gives rise to 5-methylcytosine (5MC) and 6-methylaminopurine (6MAP). The methylase preparations isolated from the cells at the stationary growth have proved to be 1.5–1.7 times as active as the enzyme from the cells at the logarithmic growth stage. The extract ofE. coli SK cells infected with the phage S_D cannot methylate DNAin vitro. This fact is due tode novo synthesis of the enzyme which disintegrates SAM down to 5-methylthioadenosine (5MTA) and homoserine (HS). This enzyme is not found in the cells infected with the S_D phage in the presence of chloroamphenicole. The activity of the enzyme which disintegrates SAM is the highest between the 4th and the 5th minutes of infection. Thus it may be assumed that this enzyme, most probably, is an early virus specific protein and preventsin vivo methylation of the phage DNA.     

Nucleotide sequence of a reiterated rat DNA fragment

A reiterated component of rat DNA was isolated by restriction with HindIII endonuclease and polyacrylamide gel electrophoresis. Sequence analysis revealed that the fragment was 179 nucleotides long. Unlike the known 370N reiterated rat DNA fragment which contained a high m5C content (2.7 mole%), this repetitive element contained a rather low m5C content (0.5 mole%). The present rat repetitive sequence appeared to be of alpha-type as shown by its significant homologies with alpha DNA sequences of African green monkey and human. The possibility of sequence heterogeneity is discussed.     

Novel methylation at GpC dinucleotide in the fish Sparus aurata genome

To date, vertebrate DNA has been found methylated at the 5 position of cytosine exclusively in dinucleotide CpG or CpNpG stretches. On the the other hand, we determined that cytosine was methylated unusually in dinucleotide GpC at 5-GGCC-3 sequences in the teleost Sparus aurata EcoRI satellite DNA family. This finding is the first example of methylated GpC sequences in the eukaryotic genomes. At this regard, we have examined the relative methylation levels at this site of the highly repetitive EcoRI satellite DNA family from Sparus aurata different tissues. The EcoRI repeat was remarkably more methylated in male germ cells but hypomethylated in female germ cells at the Hae III restriction site ( GpC). The novel modification and the differential methylation pattern suggest that EcoRI satellite could have a structural and/or functional role at the centromeres of Sparus aurata.     

Methylation sensitivity of the restriction enzymes FnuDII and AccII

The restriction enzymes FnuDII and AccII are isoschizomers of the DNA sequence 5-CGCG-3. We have determined that 5-methylcytidine at either cytidine position in this recognition sequence inhibits DNA cleavage by FnuDII and AccII. A third isoschizomer, ThaI was previously shown to exhibit an identical methylation sensitivity. It is remarkable that 3 restriction enzymes derived from diverse microbiological sources exhibit this identical methylation sensitivity.Abbreviations bp base pair(s) - m_c 5-methylcytidine - Tris-borate buffer 89 mM Tris-base, 89 mM boric acid, 2.5 mM EDTA, pH 8.3     

DNA methylation inhibits propagation of tomato golden mosaic virus DNA in transfected protoplasts

The effects of methylation on plant viral DNA replication have been studied inNicotiana tabacum protoplasts transfected with DNA of the geminivirus tomato golden mosaic virus (TGMV). The transfected cells were also used to determine whether experimentally introduced methylation patterns are maintained in extrachromosomal viral DNA. Replacement of cytosine residues with 5-methylcytosine (m⁵C) reduced the amount of viral DNA which accumulated in transfected protoplasts. The reduction was observed whether m⁵C residues were substituted for cytosine residuesin vitro in either the viral strand or the complementary strand of double-stranded circular inoculum DNAs containing tandemly repeated copies of the A component of the TGMV genome. Both limited and extensive cytosine methylation of TGMV DNA sequencesin vitro was not propagated in progeny viral DNA. The absence of detectable maintenance-type methylation of the transfecting TGMV DNA sequences may be related to the lack of methylation observed in double-stranded TGMV DNA isolated from infected plants.     

Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes

Summary The dinucleotide CpG is a hotspot for mutation in the human genome as a result of (1) the modification of the 5 cytosine by cellular DNA methyltransferases and (2) the consequent high frequency of spontaneous deamination of 5-methyl cytosine (5mC) to thymidine. DNA methylation thus contributes significantly, albeit indirectly, to the incidence of human genetic disease. We have attempted to estimate for the first time the in vivo rate of deamination of 5mC from the measured rate of 5mC deamination in vitro and the known error frequency of the cellular G/T mismatch-repair system. The accuracy and utility of this estimate (m _d ) was then assessed by comparison with clinical data, and an improved estimate of m _d (1.66x10^-16 s^-1) was derived. Comparison of the CpG mutation rates exibited by globin gene and pseudogene sequences from human, chimpanzee and macaque provided further estimates of m _d , all of which were consistent with the first. Use of this value in a mathematical model then permitted the estimation of the length of time required to produce the level of CpG suppression currently found in the bulk DNA of vertebrate genomes. This time span, approximately 450 million years, corresponds closely to the estimated time since the emergence and adaptive radiation of the vertebrates and thus coincides with the probable advent of heavily methylated genomes. An accurate estimate of the 5mC deamination rate is important not only for clinical medicine but also for studies of gene evolution. Our data suggest both that patterns of vertebrate gene methylation may be comparatively stable over relatively long periods of evolutionary time, and that the rate of CpG deamination can, under certain limited conditions, serve as a molecular clock.     

Production and characterization of somatic hybrids between upland cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis>) and wild cotton (<Emphasis Type="Italic">G. klotzschianum</Emphasis> Anderss) via electrofusion

Symmetric somatic hybrid plants between Gossypium hirsutum Coker 201 and G. klotzschianum were obtained through electrofusion. The fusion products were cultured in KM₈P medium supplemented with 2.685 M -naphthaleneacetic acid and 0.465 M kinetin, and the regenerated plants were morphologically, genetically, and cytologically characterized. Nuclear-DNA flow cytometric analysis revealed that the plants tested (31 of 40) had a relative DNA content close to the total DNA contents of the two parents. Subsequent genome DNA analysis using random amplified polymorphic DNA markers revealed 16 of 18 plants were true somatic hybrids. Cytological investigation of the metaphase root-tip cells of seven hybrids revealed there were 72–81 chromosomes in the hybrids, a value close to the expected 78 chromosomes. The morphology of the hybrids was distinct from that of the parents and from that of the regenerants from protoplasts of Coker 201. Somatic hybridization represents a potent and novel tool for transferring genomes of wild cottons containing economically important traits to cultivars in breeding programs. This is the first report on the regeneration of somatic hybrids via protoplast fusion in cotton.