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.     

Changes of enzymes and factors involved in DNA synthesis during wheat embryo germination

We have previously purified and characterized wheat germ DNA polymerases A and B. To determine the role played by DNA polymerases A and B in DNA replication, we have measured the level of their activities during wheat embryo germination. The level of cellular proteins known to be associated with DNA synthesis such as PCNA and DNA primase were also investigated. The activity of DNA polymerase A gradually increased reaching a maximal level at 12 h after germination. Three days later, only a residual activity was detected. DNA polymerase B showed the same pattern during germination with very similar changes in activity. Our results indicate a striking correlation between maximal activities of DNA polymerase A, DNA polymerase B and optimal levels of DNA synthesis. These results support a replicative role of these enzymes. The activity of wheat DNA primase that copurifies with DNA polymerase A also increases during wheat germination. Taking together all its properties, and in spite of its behaviour with some inhibitors, DNA polymerase A may be considered as the plant counterpart of animal DNA polymerase . Concerning DNA polymerase B we have previously shown that PCNA stimulates its processivity. Besides studying the changes of DNA polymerases A and B and DNA primase we have also studied changes in PCNA during germination. We show that PCNA is present in wheat embryos at a constant relatively high level during the first 24 h of germination. After 48 h, the absence of PCNA is concomitant with an important decrease in DNA polymerase B activity. In this report we confirm the behaviour of DNA polymerase B as a -like activity.Département de Biologie, Université de Drah-Lmraz,Fez, Maroc     

Early DNA synthesis during the germination of wheat embryos

Both [³H]thymidine and [³H]deoxyadenosine were found to be incorporated into the nuclear DNA of wheat embryos immediately after dry embryos were allowed to imbibe aqueous solutions of the radioactive precursors. The early labelled DNA sedimented in a manner suggesting that replicative intermediates were already formed within the first 90 min of germination. However, aphidicolin remained without any effect on this early DNA synthesis. Likewise, a cell-free system derived from early embryos incorporated [³H]dCTP into DNA independently of the presence of aphidicolin. On the contrary, dideoxyTTP inhibited the DNA synthesis considerably. It is concluded that a proportion of the resting wheat embryo cells is able to initiate a replicative DNA synthesis immediately upon imbibition. The synthesis seems, however, to proceed with the participation of a γ-like, rather than an α-like, DNA polymerase.     

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; )     

Identification of methylated sequences in genomic DNA of adult Drosophila melanogaster

The genome of Drosophila melanogaster contains methylated cytosines. Recent studies indicate that DNA methylation in the fruit fly depends on one DNA methyltransferase, dDNMT2. No obvious phenotype is associated with the downregulation of this DNA methyltransferase. Thus, identifying the target sequences methylated by dDNMT2 may constitute the first step towards understanding the biological functions of this enzyme. We used anti-5-methylcytosine antibodies as affinity column to identify the methylated sequences in the genome of adult flies. Our analysis demonstrates that components of retrotransposons and repetitive DNA sequences are putative substrates for dDNMT2. The methylation status of DNA encoding Gag, a protein involved in delivering the transposition template to its DNA target, was confirmed by sodium bisulfite sequencing.     

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.     

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.     

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.     

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.     

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/.     

Increase of natural benzodiazepines in wheat and potato during germination

Aqueous acid extracts of wheat grains and potato exhibit after HPLC separation a series of compounds that are able to inhibit the binding of benzodiazepines to benzodiazepine receptors of rat brain membranes. In wheat one of the inhibiting compounds was shown to be identical to diazepam by means of HPLC characterization and gas chromatography combined with mass spectrometry. In potato one of the most prominent components in terms of binding inhibiting activity was identified as lormetazepam. In wheat and potato germination increases total inhibiting activity of the whole plant extracts as well as the content of the benzodiazepines approximately by factor five. Because uptake of benzodiazepines from the surrounding was excluded these findings indicate the biosynthesis of the benzodiazepines diazepam and lormetazepam by the plants investigated.     

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.     

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.