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.     

Analysis of DNA methylation during the germination of wheat seeds

DNA methylation is known to play a crucial role in regulating plant development and organ or tissue differentiation. Here, we focused on the DNA methylation dynamics during the germination of wheat seeds using the adapted AFLP technique so called methylation-sensitive amplified polymorphism (MSAP). The MSAP profiles of genomic DNA in embryo and endosperm tissues of germinating seeds, as well as dry seeds were characterized and notable changes of cytosine methylation were detected. Comparisons of MSAP profiles in different tissues tested showed that the methylation level in dry seeds is the highest. The alteration analysis of cytosine methylation displayed that the number of demethylation events were three times higher than that of de novo methylation, which indicated that the demethylation was predominant in germinating wheat seeds, though the methylation events occurred as well. Sixteen differentially displayed DNA fragments in MSAP profiles were cloned and the sequencing analysis confirmed that nine of them contained CCGG sites. The further BLAST search showed that four of the cloned sequences were located in coding regions. Interestingly, three of the sixteen candidates were homologous to retrotransposons, which indicated that switches between DNA methylation and demethylation occurred in retrotransposon elements along with the germination of wheat seeds.     

Changes in hybridizable RNA in winter wheat embryos during germination and vernalization

DNA-RNA hybridization-competition experiments were performedto analyze RNA heterogeneity in wheat embryos during germinationand vernalization. A significant difference was found betweenRNA populations of 24-hr and 3-day germinated embryos, whileminor differences were detected between 3- and 5-day germinatedembryo RNAs and between 20- and 40-day cold-treated embryo RNAs.RNA populations in 30-day cold-treated embryos were significantlydifferent from those in 50-day ones. The RNA species presentin 50-day cold-treated embryos were not similar to those in3- and 5-day germinated embryos. A great portion of the RNAspecies in 3-day germinated embryos was found in 30-day cold-treatedembryos. These results suggested that some new RNA species aresynthesized in wheat embryos during 30 to 50 days of cold treatment. ¹ Present address: Department of Biochemistry, Faculty of PharmaceuticalSciences, Higashi Nippon Gakuen University, Ishikari-Tobetsu,Hokkaido 061–02, Japan. (Received February 21, 1977; )     

Rna synthesis during the germination of wheat seed

Incorporation of [¹⁴C]uridine into various RNA fractions of germinating wheat embryo was studied. During the first 3 hr of germination the precursor was incorporated predominantly into a specific component of the RNA (messenger RNA). Neither ribosomal nor transfer RNA were labeled at this time. It is concluded that biosynthetic processes are resumed after the breaking of dormancy in a sequential manner. This sequence begins with the initiation of messenger RNA synthesis.     

The sequence of initiation of RNA, DNA and protein synthesis in the wheat grains during germination

The syntheses of main macromolecular substances, in a whole wheat grain allowed to germinate, are triggered in the following order: RNA, protein, DNA. The RNA synthesis, as judged by [2-¹⁴C]uridine incorporation, is initiated almost immediately after the seeds are exposed to the optimal germination conditions, whereas [1-¹⁴C]leucine and [2-¹⁴C]thymidine incorporation begins to occur only 3 and 4 hr later, respectively. The initiation of protein synthesis is accompanied by an apparent cessation of uridine incorporation.     

Detection of methylated sequences in eukaryotic DNA with the restriction endonucleases Smai and Xmai

araC protein was identified on two-dimensional O'Farrell gels (O'Farrell, 1975) as a protein electrophoresing as two spots, both of molecular weight 30,500 and pI near 7.1, but differing by about 0.1 pH unit. The two spots were seen in crude extracts from cells overproducing C protein as specified by a plasmid, by a phage, and were also seen in C protein purified to about 20% purity on the basis of biological activity. A label-chase experiment indicated that both species of araC are unstable in vivo and possess half-lives of about 60 minutes. The normal intracellular level of C protein is about 40 monomers per cell.     

Prediction of methylated CpGs in DNA sequences using a support vector machine

DNA methylation plays a key role in the regulation of gene expression. The most common type of DNA modification consists of the methylation of cytosine in the CpG dinucleotide. At the present time, there is no method available for the prediction of DNA methylation sites. Therefore, in this study we have developed a support vector machine (SVM)-based method for the prediction of cytosine methylation in CpG dinucleotides. Initially a SVM module was developed from human data for the prediction of human-specific methylation sites. This module achieved a MCC and AUC of 0.501 and 0.814, respectively, when evaluated using a 5-fold cross-validation. The performance of this SVM-based module was better than the classifiers built using alternative machine learning and statistical algorithms including artificial neural networks, Bayesian statistics, and decision trees. Additional SVM modules were also developed based on mammalian- and vertebrate-specific methylation patterns. The SVM module based on human methylation patterns was used for genome-wide analysis of methylation sites. This analysis demonstrated that the percentage of methylated CpGs is higher in UTRs as compared to exonic and intronic regions of human genes. This method is available on line for public use under the name of Methylator at http://bio.dfci.harvard.edu/Methylator/.     

Tissue specific differentially methylated regions (TDMR): Changes in DNA methylation during development

Tissue specific differentially methylated regions (TDMRs) were identified and localized in the mouse genome using second generation virtual RLGS (vRLGS). Sequenom MassARRAY quantitative methylation analysis was used to confirm and determine the fine structure of tissue specific differences in DNA methylation. TDMRs have a broad distribution of locations to intragenic and intergenic regions including both CpG islands, and non-CpG islands regions. Somewhat surprising, there is a strong bias for TDMR location in non-promoter intragenic regions. Although some TDMRs are within or close to repeat sequences, overall they are less frequently associated with repetitive elements than expected from a random distribution. Many TDMRs are methylated at early developmental stages, but unmethylated later, suggesting active or passive demethylation, or expansions of populations of cells with unmethylated TDMRs. This is notable during postnatal testis differentiation where many testis specific TDMRs become progressively "demethylated". These results suggest that methylation changes during development are dynamic, involve demethylation and methylation, and may occur at late stages of embryonic development or even postnatally.     

Musa methylated DNA sequences associated with tolerance toMycosphaerella fijiensis toxins

DNA methylation is an epigenetic phenomenon associated with gene silencing in transgenic plants, retrotransposons and virus infection. Expression analysis of specific genes in Arabidopsis methylation mutants showed an association between DNA methylation and gene expression. To determine whether DNA methylation is associated with resistance to black Sigatoka (BS) andMycosphaerella fijiensis (MF), we used anin vitro assay of mesophyll cell suspensions of reference cultivars with known resistance to BS. Methylation of CC^mGG sequences was evaluated by methylation-sensitive amplification polymorphism (MSAP) markers of reference cultivars and somaclonal variants to identify molecular markers associated with resistance to MF toxins and BS. Four MSAP markers were associated with resistance (MAR) to MF toxins. The MSAP markers show a high degree of sequence similarity with resistance gene analog and with retrotransposon sequences. The MSAP markers are useful as molecular indicators of tolerance to MF toxins and resistance to BS.     

Asparaginyl endopeptidase during maturation and germination of durum wheat

Asparaginyl-endopeptidase activity was detected in endosperms of maturing and germinating wheat seeds. The highest activity was found during maturation before the maximal accumulation of storage proteins. The enzyme activity then decreased in the dry seeds and increased again during germination. The increase of activity during germination required the presence of the embryo. In fact, the activity found in detached endosperms was lower than that found in attached ones. The localization at tissue level of the enzyme reveals differences between maturation and germination: the enzyme was about equally located in the aleurone layer and starchy endosperm during maturation, but solely in the aleurone layer during germination. The asparaginyl enzymes from maturing and germinating seeds had many similar properties, such as pH optimum, pH stability, thermal stability and sensitivity to thiol reagents and to thiol compounds. The results suggest that asparaginyl endopeptidases may be involved in the modification of proproteins of storage proteins during seed maturation and in the degradation of storage proteins deposited in the aleurone layer during germination.     

Changes in polyamine concentration during seed germination

Phaseolus mungo seeds 0 to 10 days after germination contained putrescine, spermidine, spermine, cadaverine, agmatine and tyramine. The rate of biosynthesis of total polyamines, proteins and RNA in the developing seeds follows similar profiles, reaching maxima 3 hr from germination. Putrescine, cadaverine, spermidine, spermine and agmatine were the major amines found in Pisum sativum 0–7 days after germination. RNA and proteins seem to follow the same pattern as polyamines during the first 12 hr in the developing pea seeds. RNA reaches a peak at 15 hr and polyamines and proteins peak 24 hr after germination. A rise to total polyamine concentration was also observed in seeds of Tragopogon porrifolius, Zea mays and Triticum aestivum 2–12 hr after germination.     

Headloop suppression PCR and its application to selective amplification of methylated DNA sequences

Selective amplification in PCR is principally determined by the sequence of the primers and the temperature of the annealing step. We have developed a new PCR technique for distinguishing related sequences in which additional selectivity is dependent on sequences within the amplicon. A 5′ extension is included in one (or both) primer(s) that corresponds to sequences within one of the related amplicons. After copying and incorporation into the PCR product this sequence is then able to loop back, anneal to the internal sequences and prime to form a hairpin structure—this structure is then refractory to further amplification. Thus, amplification of sequences containing a perfect match to the 5′ extension is suppressed while amplification of sequences containing mismatches or lacking the sequence is unaffected. We have applied Headloop PCR to DNA that had been bisulphite-treated for the selective amplification of methylated sequences of the human GSTP1 gene in the presence of up to a 10⁵-fold excess of unmethylated sequences. Headloop PCR has a potential for clinical application in the detection of differently methylated DNAs following bisulphite treatment as well as for selective amplification of sequence variants or mutants in the presence of an excess of closely related DNA sequences.     

Comparative salt tolerance in triticale,wheat and rye during germination

Summary Differences in salt tolerance of wheat and barley have been observed but knowledge of such differences in triticale (X Triticosecale Wittmack) cultivars is of potential importance. Effects of six salinity levels (0 to 2% NaCl) on germination of triticales Beagle and 6TA 131 in comparison to wheat and rye were determined at 15–20°C. Beagle triticale and rye showed similar trends in germination reduction as salinity increased from 0 to 1.5% NaCl and exhibited fairly high salt tolerance. However, 6TA 131 triticale and wheat showed a significant drop in germination even at 0.5% NaCl concentration and were more susceptible to salt injury.     

KAISO--a new member of the BTB/POZ family specifically bindsto methylated DNA sequences

A protein specifically binding a symmetrically methylated DNA fragment of the first intron of the mts1 gene was studied. The protein was purified by gel filtration and affinity chromatography. Mass spectrometry showed that the protein is Kaiso, a new member of the BTB/POZ family. To study the association with methylated DNA sequences in vivo, the location of Kaiso in NIH 3T3 cells was analyzed. Immunofluorescent staining with polyclonal antibodies against Kaiso showed that the protein is predominantly associated with the nucleoli. The causes of its distribution awaits further investigation. The zinc-finger domains of Kaiso were for the first time demonstrated to specifically recognize symmetrically methylated DNA sequences in vitro.     

Changes in population structure of the soilborne fungus Gaeumannomyces graminis var. tritici during continuous wheat cropping

A method was developed to assess the genetic structure of Gaeumannomyces graminis var. tritici (Ggt) populations and test the hypothesis of an association between disease level in the field with changes in pathogen populations. A long-term wheat monoculture experiment, established since 1994, generated different take-all epidemics with varying the number of wheat crop successions in the 1999-2000 cropping season. Genetic polymorphism in Ggt populations was investigated over natural, local epidemics. Four populations of 30 isolates were isolated from necrotic wheat roots in a first, third, fourth, and sixth wheat crop in the same year. Each Ggt isolate was characterized with RAPD (Random Amplification Polymorphism DNA) markers and AFLP (Amplified Fragment Length Polymorphism) fingerprinting. Seventeen multilocus genotypes based on the combination of RAPD and AFLP markers were identified among all these populations. The 120 isolates were divided into two main groups, G1 and G2, according to bootstrap values higher than 86%, except for an unique isolate from the third wheat crop. Within each group, populations ranged between 93 and 100% similarity. Both groups included isolates collected from the first, third, fourth or sixth wheat crop. However, G1 group profiles dominated amongst isolates sampled in the first and the sixth wheat crops, whereas G2 group profiles largely dominated amongst isolates collected from the third and fourth wheat crops. Aggressiveness of group G2 (38%) was significantly greater than that of G1 (29.5%). These results suggest that changes in Ggt population structure occur during continuous wheat cropping. The distinction of two Ggt groups provides a simple basis for further spatio-temporal analysis of Ggt population during polyetic take-all decline.     

Characterization of inverted repeated sequences in wheat nuclear DNA.

The properties of inverted repeated sequences in wheat nuclear DNA have been studied by HAP(1) chromatography, nuclease S1 digestion and electron microscopy. Inverted repeated sequences comprise 1.7% of wheat genome. The HAP studies show that the amount of "foldback HAP bound DNA" depends on DNA length. Inverted repeats appear to be clustered with an average intercluster distance of 25 kb. It is estimated that there are approximately 3 x 10(6) inverted repeats per haploid wheat genome. The sequences around inverted repeats involve all families of repetition frequencies. Inverted repeats are observed as hairpins in electron microscopy. 20% of hairpins are terminated by a single-stranded spacer ranging from 0.3 to 1.5 kb in length. Duplex regions of the inverted repeats range from 0.1 to 0.45 kb with number average values of 0.24 kb and 0.18 kb for unlooped and looped hairpin respectively. Thermal denaturations and nuclease S1 digestions have revealed a length of about 100 bases for duplex regions. The methods used to study inverted repeated sequences are compared and discussed.     

Changes in the permeability of ascospores of Neurospora tetra-sperma during germination

The respiration and germination of activated ascospores of Neurospora tetrasperma have been shown to be almost completely inhibited by concentrations of ethylene diaminetetraacetic acid (EDTA) as low as 0.0035 M. In contrast, however, dormant ascospores are insensitive to this chelating agent. At any time up to about 150 minutes after activation Ca(++) or Mg(++) can completely reverse this toxicity but Cu(++), Co(++), and Mn(++) only partially reverse it. After this time, the minerals of the Neurospora "minimal" medium taken singly, or in various combinations cannot reverse this effect. Adding EDTA at 120 minutes after activation eliminates the lag period associated with its effect upon respiration. Inhibition occurs even though the cells seem to be impermeable to EDTA. Cationic exchange resins, as another example of a non-penetrating metal-binding agent, gave effects similar to those noted with EDTA. Of the resins used the H(+) form of IR-120 and the Na(+) and K(+) forms of amberlite IRC-50 were the most toxic to activated ascospores. On the other hand, dormant ascospores were entirely unaffected by the resins. The release of Ca(++) from activated ascospores coincided with the period of maximum sensitivity to EDTA. More than 60 per cent of the cell's content of K(+) is released by EDTA-inhibited ascospores. A low pH decreased the effectiveness of EDTA as a poison. The data are consistent with the possibility that non-penetrating metal-binding agents are toxic because of the irreversible removal of essential cations from the cell. The kinetic data for the inhibitory effects, and for the release of Ca(++) establish that the permeability of germinating ascospores to minerals changes drastically as a result of activation.