逆境处理和DNA甲基化影响柑橘体细胞胚发生

对 1 5种柑橘胚性愈伤组织进行体细胞胚诱导 ,发现逆境处理有利于体细胞胚发生 ,并可以恢复部分品种的体细胞胚发生能力。对具有和失去体细胞胚发生能力的两种纽荷尔脐橙 (CitrussinensisOsb .)愈伤组织进行随机扩增多态性DNA (RAPD)分析没有检测到带型的差异 ,而对它们的甲基化敏感扩增多态性 (MSAP)进行分析则发现两种愈伤组织间具有明显的DNA甲基化差异 ,具体细胞胚发生能力的愈伤组织的甲基化水平较失去体细胞胚发生能力的低     

Genetically stable regeneration of apple plants from slow growth

Shoot-tips of apple cultivar `Gala' were stored in vitrousing a low temperature slow-growth culture method. All shoot-tips survived 1-year storage, with a significant height increment over that period. Eight `Gala' single-bud sibling lines were established for genetic analysis. Although cytological examination detected chromosomal variation in plants recovered from slow growth culture, the ploidy remained genetically stable relative to the before-storage cultures. An amplified fragment length polymorphism (AFLP) assay was performed to detect DNA sequence variation. No differences in the DNA fragment patterns were observed using 20 primer combinations between the before-storage and the stored samples. In addition, a methylation sensitive amplified polymorphism (MSAP) assay was performed to investigate the DNA methylation status in both the before-storage and stored samples. It was found that the slow-growth storage resulted in a significant DNA methylation change in the stored shoots compared with the before-storage samples.     

Epigenetic variation in the callus of <Emphasis Type="Italic">Brassica napus</Emphasis> under different inducement conditions

Tissue culture, a traditional technique broadly used for the genetic transformation and functional verification of target genes, induces epigenetic variations in transgenic acceptors of plants. This study compared the DNA methylation patterns during the callus formation of Brassica napus induced by different concentrations of 6-BA and 2,4-D through methylation-sensitive amplification polymorphism. The highest induction rate (85%) was observed in the hypocotyls cultured with 0.1 mg/L 2,4-D and the lowest methylation rate (25.09%) was detected in the hypocotyls cultured with 1.0 mg/L 6-BA. The methylation rates of the callus cultured with 0.2 and 0.05 mg/L 2,4-D were 29.99 and 28.31%, respectively. The callus induction rates were reduced to 79 and 80%. The methylation rates of the callus induced by 2.0 and 0.5 mg/L 6-BA were 28.17 and 33.98%, respectively. The callus induction rates were reduced to 76 and 74%. The expression analysis of methyltransferase under different induction conditions agreed with methylation modifications; therefore, the effects of hormones on callus induction may be partially indicated by methylation changes in B. napus genome.     

Tissue culture-induced DNA methylation polymorphisms in repetitive DNA of tomato calli and regenerated plants

The propagation of plants through tissue culture can induce a variety of genetic and epigenetic changes. Variation in DNA methylation has been proposed as a mechanism that may explain at least a part of these changes. In the present study, the methylation of tomato callus DNA was compared with that of leaf DNA, from control or regenerated plants, at MspI/HpaII sites around five middle-repetitive sequences. Although the methylation of the internal cytosine in the recognition sequence CCGG varied from zero to nearly full methylation, depending on the probe used, no differences were found between callus and leaf DNA. For the external cytosine, small differences were revealed between leaf and callus DNA with two probes, but no polymorphisms were detected among DNA samples of calli or DNA samples of leaves of regenerated plants. When callus DNA cut with HindIII was studied with one of the probes, H9D9, most of the signal was found in high-molecular-weight DNA, as opposed to control leaf DNA where almost all the signal was in a fragment of 530 bp. Also, an extra fragment of 630 bp was found in the callus DNA that was not present in control leaf DNA. Among leaves of plants regenerated from tissue culture, the 630-bp fragment was found in 10 of 68 regenerated plants. This 630-bp fragment was present among progeny of only 4 of these 10 plants after selfing, i.e. it was partly inherited. In these cases, the fragment was not found in all progeny plants, indicating heterozygosity of the regenerated plants. The data are interpreted as indicating that a HindIII site becomes methylated in callus tissue, and that some of this methylation persists in regenerated plants and is partly transmitted to their progeny.     

Rapid changes in amplification and methylation pattern of genomic DNA in cultured carrot root explants (Daucus carota L.)

Summary Rapid genomic DNA variation due to methylation and copy number alteration was observed in carrot root explants 6 h after inoculation and during a 36-h period of exponential callus growth. De novo methylation and amplification of restricted BspNI fragments of low molecular weight occurred before cell cycle activation and should, therefore, be independent of progression through the S-phase of the cell cycle. Growth regulators seemed to influence the amplification pattern indirectly by regulating cell division activity. In exponentially growing callus tissue the copy number of most of the repetitive fragments was dramatically reduced. It is presumed that this reduction in the copy number of repetitive fragments is characteristic of rejuvenilization. 3-Indole-acetic-acid (IAA) and inositol in the medium increased the degree of unspecific genomic DNA methylation in growing rhizogenic carrot callus tissue in the absence of kinetin, which inhibits root induction at that stage. A possible relation to the induction of rhizogenesis is considered. The observed reduction in number of repetitive restriction fragments and the increase in DNA methylation are gross changes covering the total genome. The results are discussed in relation to the controversy concerning the general biological significance of the methylation and amplification of DNA sequences.     

The detection of genome polymorphism in Stachys species using RAPD

Molecular genome analysis was for the first time carried out in the genus Stachys. RAPD analysis proved to be suitable for identifying the species-specific markers, studying the interspecific DNA polymorphism, and detecting the genetic changes that arise during in vitro culturing of Stachys sieboldii. In addition, RAPD was used for screening genetic variation in S. sieboldii regenerants obtained at various phytohormone concentrations. High cytokinin concentrations and multiple regeneration were shown to induce genetic changes detectable with RAPD patterns. High DNA polymorphism was demonstrated for two types of S. sieboldii callus cultures and for plants regenerated from a callus culture.     

Detection of DNA methylation pattern in thidiazuron-induced blueberry callus using methylation-sensitive amplification polymorphism

During the normal developmental process, programmed gene expression is an essential phenomenon in all organisms. In eukaryotes, DNA methylation plays an important role in the regulation of gene expression. The extent of cytosine methylation polymorphism was evaluated in leaf tissues collected from the greenhouse grown plants and in in vitro-derived callus of three lowbush and one hybrid blueberry genotypes, using methylation-sensitive amplification polymorphism (MSAP) technique. Callus formation started from the leaf segments after 4 weeks of culture on a thidiazuron (TDZ) containing medium. Maximum callus formation (98 %) was observed in the hybrid blueberry at 1.0 mg dm^-3 TDZ. Although noticeable changes in cytosine methylation pattern were detected within the MSAP profiles of both leaf and callus tissues, methylation events were more polymorphic in calli than in leaf tissues. The number of methylated CCGG sites varied significantly within the genotypes ranging from 75 to 100 in leaf tissues and from 215 to 258 in callus tissues. Differences in the methylation pattern were observed not only in a tissue-specific manner but also within the genotype in a treatment specific manner. These results demonstrated the unique effect of TDZ and the tissue culture process on DNA methylation during callus development.     

Genome-Scale Discovery of DNA-Methylation Biomarkers for Blood-Based Detection of Colorectal Cancer

Background

There is an increasing demand for accurate biomarkers for early non-invasive colorectal cancer detection. We employed a genome-scale marker discovery method to identify and verify candidate DNA methylation biomarkers for blood-based detection of colorectal cancer.

Methodology/Principal Findings

We used DNA methylation data from 711 colorectal tumors, 53 matched adjacent-normal colonic tissue samples, 286 healthy blood samples and 4,201 tumor samples of 15 different cancer types. DNA methylation data were generated by the Illumina Infinium HumanMethylation27 and the HumanMethylation450 platforms, which determine the methylation status of 27,578 and 482,421 CpG sites respectively. We first performed a multistep marker selection to identify candidate markers with high methylation across all colorectal tumors while harboring low methylation in healthy samples and other cancer types. We then used pre-therapeutic plasma and serum samples from 107 colorectal cancer patients and 98 controls without colorectal cancer, confirmed by colonoscopy, to verify candidate markers. We selected two markers for further evaluation: methylated THBD (THBD-M) and methylated C9orf50 (C9orf50-M). When tested on clinical plasma and serum samples these markers outperformed carcinoembryonic antigen (CEA) serum measurement and resulted in a high sensitive and specific test performance for early colorectal cancer detection.

Conclusions/Significance

Our systematic marker discovery and verification study for blood-based DNA methylation markers resulted in two novel colorectal cancer biomarkers, THBD-M and C9orf50-M. THBD-M in particular showed promising performance in clinical samples, justifying its further optimization and clinical testing.     

DNA repair and STR PCR amplification from damaged DNA of human bloodstains

Detection and identification of DNA structure from aged and damaged biological materials such as bloodstain are important for human genetic study and individual identification. However, after a long period of storage, the DNA structure of biological samples is degraded to various degrees depending on several factors including environmental condition. In this study, human bloodstains that have been stored at room temperature for one to 39 years were used to represent damaged biological samples. The numbers of apurinic/apyrimidinic sites (AP sites) were investigated by the DNA Damage Quantification Kit to evaluate the lesions in DNA structure. The damaged DNA from the stored human bloodstains was repaired using seven DNA repair enzymes. As DNA genetic marker, short tandem repeat (STR) genotypes were amplified using the non-repaired and repaired DNA preparations from the stored bloodstains. The results indicated that the number of AP sites increased as the storage time increased. While only 2 to 6 STR loci were detected in the damaged DNA of bloodstains stored for over 30 years, after DNA repair all the genotypes in the STR system could be analyzed even from bloodstains that had been stored for the longest period.     

DNA methylation of retrotransposons,DNA transposons and genes in sugar beet (Beta vulgaris L.)

The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses the activity of transposable elements (TEs), affects gene expression and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of worldwide sugar needs, has a relatively small genome size (758 Mbp) consisting of approximately 485 Mbp repetitive DNA (64%), in particular satellite DNA, retrotransposons and DNA transposons. Genome‐wide cytosine methylation in the sugar beet genome was studied in leaves and leaf‐derived callus with a focus on repetitive sequences, including retrotransposons and DNA transposons, the major groups of repetitive DNA sequences, and compared with gene methylation. Genes showed a specific methylation pattern for CG, CHG (H = A, C, and T) and CHH sites, whereas the TE pattern differed, depending on the TE class (class 1, retrotransposons and class 2, DNA transposons). Along genes and TEs, CG and CHG methylation was higher than that of adjacent genomic regions. In contrast to the relatively low CHH methylation in retrotransposons and genes, the level of CHH methylation in DNA transposons was strongly increased, pointing to a functional role of asymmetric methylation in DNA transposon silencing. Comparison of genome‐wide DNA methylation between sugar beet leaves and callus revealed a differential methylation upon tissue culture. Potential epialleles were hypomethylated (lower methylation) at CG and CHG sites in retrotransposons and genes and hypermethylated (higher methylation) at CHH sites in DNA transposons of callus when compared with leaves.     

Effect of antioxidants on the genetic stability of cryopreserved mint shoot tips by encapsulation–dehydration

The effect of antioxidants applied in one step of a cryopreservation protocol by encapsulation–dehydration on recovery and genetic stability of mint shoot tips has been studied. Glutathione (0.16 or 0.24 mM), ascorbic acid (0.28 or 0.43 mM) and α-tocopherol (vitamin E) were added to the preculture medium (0.3 M sucrose). DNA was extracted from three different types of samples: leaves from shoots, callus at the base of shoots and callus. RAPD and AFLP markers were used to assess the genetic stability. The use of antioxidants did not improve recovery after cryopreservation. One of the genotypes, ‘MEN 198’, showed higher percentage of stable samples than the other one, ‘MEN 186’ (56 vs. 37?%; considering all treatments and types of explant). The use of vitamin E improved the percentage of stable samples with respect to control treatment (no antioxidant) in ‘MEN 186’. No differences in the percentages of stable samples were observed among cryopreserved and non-cryopreserved (treated similarly without immersion in liquid nitrogen) plant material. Recovered shoots of both genotypes showed higher stability (76–80?% stable samples) than callus samples (14–22?%).     

Genetic and epigenetic stability of cryopreserved and cold-stored hops (Humulus lupulus L.)

Conventional cold storage and cryopreservation methods for hops (Humulus lupulus L.) are available but, to our knowledge, the genetic and epigenetic stability of the recovered plants have not been tested. This study analyzed 51 accessions of hop using the molecular techniques, Random Amplified DNA Polymorphism (RAPD) and Amplified Fragment Length Polymorphism (AFLP), revealing no genetic variation among greenhouse-grown controls and cold stored or cryopreserved plants. Epigenetic stability was evaluated using Methylation Sensitive Amplified Polymorphism (MSAP). Over 36% of the loci were polymorphic when the cold and cryo-treated plants were compared to greenhouse plants. The main changes were demethylation events and they were common to the cryopreserved and cold stored plants indicating the possible effect of the in vitro establishment process, an essential step in both protocols. Protocol-specific methylation patterns were also detected indicating that both methods produced epigenetic changes in plants following cold storage and cryopreservation.     

PCR-based methylation testing for Prader-Willi or Angelman syndromes using archived fixed-cell suspensions

All Prader-Willi syndrome (PWS) and 75% of Angelman syndrome (AS) patients have specific DNA methylation pattern alterations that can be used for diagnostic evaluation. The methylation testing identifies a significantly higher proportion of patients as compared to fluorescence in situ hybridization (FISH)-based microdeletion analysis and is thus a useful diagnostic evaluation for clinically suspect, but FISH-negative, patients. We used two independent PCR-based protocols for methylation testing on fixed cell specimens archived after FISH analyses. Changes in DNA methylation due to the procedure of cell fixation were ruled out by testing control specimens before and after fixation. Then methylation testing was carried out on 20 standard fixed-cell supsensions from people suspected for PWS or AS. These fixed specimens were stored after negative FISH analysis for up to 4 years at 4 degrees C in 3:1 methanol/acetic acid. Methylation patterns associated with AS (one specimen) and with PWS (one specimen) were identified for both protocols. The observed methylation patterns were concordant with the phenotypes of the positive individuals and for the two protocols used. We have, thus, shown that archived fixed-cell suspensions from individuals suspected as PWS or AS that were negative for cytogenetic/FISH microdeletions, can now be re-evaluated with PCR-based methylation testing without the need for additional blood samples from the previously studied individuals.     

Patterns of inheritance with RAPD molecular markers reveal novel types of polymorphism in the honey bee

Summary The polymerase chain reaction (PCR) was used to generate random amplified polymorphic DNA (RAPD) from honey bee DNA samples in order to follow the patterns of inheritance of RAPD markers in a haplodiploid insect. The genomic DNA samples from two parental bees, a haploid drone and a diploid queen, were screened for polymorphism with 68 different tennucleotide primers of random sequence. Parents were scored for the presence or absence of individual bands. An average of 6.3 bands and 1.3 polymorphisms for presence/absence were observed per primer between the parents. Thirteen of these primers were used to determine the inheritance of RAPD marker alleles in the resulting progeny and in haploid drones from a daughter queen. Four types of polymorphisms were observed. Polymorphisms for band presence/absence as well as for band brightness were inherited as dominant markers, meeting Mendelian expectations in haploid and diploid progeny. Polymorphisms for fragment-length were also observed. These segregated in a near 11 ratio in drone progeny. The last type of polymorphism was manifested as a diploid-specific band. Mixing of amplification products after PCR showed that the diploid-specific band was the result of heteroduplex formation from the DNA of alternate alleles in heterozygotes. In two of the four cases of heteroduplex formation, the alternative alleles were manifested as small fragment-length polymorphisms, resulting in co-dominant markers. This is the first demonstration that a proportion of RAPD markers are not inherited in a dominant fashion.     

Global DNA Hypomethylation in Liver Cancer Cases and Controls: A Phase I Preclinical Biomarker Development Study

Background: Global genomic DNA hypomethylation is a feature of genomic DNA derived from solid and hematologic tumors in animal models and human carcinogenesis. Global genomic DNA hypomethylation may be the earliest epigenetic change from a normal to a pre-malignant cell. Objectives: To test if global hypomethylation is a good marker for early detection of cancer we used a novel quantification method of 2’-deoxynucleosides to evaluate DNA methylation in liver cancer cases and controls. Methods: Frozen tissue from liver cancer patients and controls were obtained from the Cooperative Human Tissue Network. DNA was extracted using standard methods. Genomic DNA samples were boiled and treated with nuclease P1 and alkaline phosphatase. Global genomic DNA methylation patterns were obtained using HPLC for fraction separation and mass spectrometry for quantification. A two-sample t test was performed using Welch’s approximation for samples with unequal variances. A Wilcoxon rank sum test was also performed. Results: A global genomic DNA methylation index measuring methylated cytidine relative to global cytidine in the genome was significantly lower (p-value = 0.001) for all cases, mean = 2.43 (95% CI, 2.08, 2.78), when compared to controls, mean = 3.55 (95% CI, 3.16, 3.93). Discussion: A correlation between global genomic DNA methylation patterns and type of liver tissue was observed. These results add to the accumulating body of evidence suggesting that global DNA hypomethylation may be a useful biomarker to distinguish between liver cancer cases and controls.     

RAPD markers to evaluate callus tissue of Cereus peruvianus Mill. (Cactaceae) maintained in different growth regulator combinations

RAPD markers were used to detect DNA polymorphisms in callus tissues maintained at different auxin and cytokinin combinations. There is a higher level of genetic variablity in callus tissue maintained with the highest kinetin versus 2, 4-D concentration. Callus tissues subcultured in a 4.0 mg/L 2,4-D and 4.0 mg/L kinetin combination showed high similarity and can be recommended as more suitable sources for industrial procedures of extraction of natural products such as secondary metabolites since extraction protocols can be easily standardized using genetically uniform materials. The higher genetic diversity in callus tissues of C. peruvianus cultured at 4.0 mg/L 2,4-D and 8.0 mg/L kinetin indicates this tissue as a matrix for in vitro selection of cell lines for higher natural products production. RAPD markers are, therefore, effective tools useful for detecting DNA polymorphism in callus tissue as well as in the DNA identification of callus tissues maintained in different auxin and cytokinin combinations.     

<Emphasis Type="Italic">BMP3</Emphasis> promoter hypermethylation in plasma-derived cell-free DNA in colorectal cancer patients

Detecting cfDNA in plasma or serum could serve as a ‘liquid biopsy’, for circulating tumor DNA with aberrant methylation patterns offer a possible method for early detection of several cancers which could avoid the need for tumor tissue biopsies. Bone Morphogenetic Protein 3 (BMP3) was identified as a candidate tumor suppressor gene putatively down-regulated in colorectal cancer (CRC). In this study, we aimed to assess the potential role of BMP3 promoter methylation changes in plasma DNA for detection of colorectal cancerous and precancerous lesions. Plasma DNA samples were extracted from 50 patients with histologically diagnosed polyps or tumor and 50 patients reported negative for polyps or tumors. The procedure consists of bisulfite conversion of the extracted DNA, purification of bis-DNA, and BMP3 methylation status analysis by using the bisulfite specific high resolution melting analysis. This study demonstrated that there was a significantly higher frequency of BMP3 methylated DNA in plasma in patients with polyps versus healthy controls with a sensitivity and specificity of 40 and 94%, respectively. In conclusion, our results demonstrated that BMP3 DNA methylation in plasma had not have sufficient sensitivity and it should be used in combination with other biomarkers for the detection of CRC.     

Measurement of the extent of somaclonal variation in begonia plants regenerated under various conditions. Comparison of three assays

Begonia plants were regenerated from leaf explants treated with increasing concentrations of the chemical mutagen nitrosomethylurea (NMU). In these plants, we evaluated three methods to assess the extent of variation: a qualitative, phenotypic assay (the percentage of aberrant plants), a molecular assay (changes in RAPD patterns) and a quantitative, phenotypic assay (variation in a quantitative trait). The qualitative, phenotypic assay required a large number of plants per treatment (approx. 100) and careful, skilled judgement. It was sensitive to physiological variation. The RAPD assay was not sufficiently sensitive: even at the highest NMU concentration there were no changes in RAPD patterns. The quantitative, phenotypic assay gave the best results: it was simple, objective and sensitive, and required few plants per treatment (approx. 30). Plants were also regenerated from different types of intermediate callus, and their variation was assessed. The performance of the three assays was essentially the same as with plants obtained after mutagenesis with NMU. An intermediate nodular- or non-nodular-callus phase resulted in slightly or strongly increased variation, respectively. In contrast to NMU-induced variation, callus-related variation, as determined in the quantitative, phenotypic assay, appeared to be to a large extent transient since it decreased strongly after a second direct-regeneration step. An intermediate callus phase resulted in 2.5% juvenile plants. This aberration, which might be related with changes in the methylation status of DNA, was not observed in NMU-treated plants. Received: 30 January 2000 / Accepted: 14 April 2000     

The Detection of Genome Polymorphism in Stachys Species Using RAPD

Molecular genome analysis was for the first time carried out in the genus Stachys. RAPD analysis proved to be suitable for identifying the species-specific markers, studying the interspecific DNA polymorphism, and detecting the genetic changes that arise during in vitro culturing of Stachys sieboldii. RAPD was also used for screening genetic variation in S. sieboldii regenerants obtained at various phytohormone concentrations. High cytokinin concentrations and multiple regeneration were shown to induce genetic changes detectable in RAPD patterns. High DNA polymorphism was detected for two types of S. sieboldii callus cultures and for plants regenerated from a callus culture.     

Blood diagnostic biomarkers for major depressive disorder using multiplex DNA methylation profiles: discovery and validation

Aberrant DNA methylation in the blood of patients with major depressive disorder (MDD) has been reported in several previous studies. However, no comprehensive studies using medication-free subjects with MDD have been conducted. Furthermore, the majority of these previous studies has been limited to the analysis of the CpG sites in CpG islands (CGIs) in the gene promoter regions. The main aim of the present study is to identify DNA methylation markers that distinguish patients with MDD from non-psychiatric controls. Genome-wide DNA methylation profiling of peripheral leukocytes was conducted in two set of samples, a discovery set (20 medication-free patients with MDD and 19 controls) and a replication set (12 medication-free patients with MDD and 12 controls), using Infinium HumanMethylation450 BeadChips. Significant diagnostic differences in DNA methylation were observed at 363 CpG sites in the discovery set. All of these loci demonstrated lower DNA methylation in patients with MDD than in the controls, and most of them (85.7%) were located in the CGIs in the gene promoter regions. We were able to distinguish patients with MDD from the control subjects with high accuracy in the discriminant analysis using the top DNA methylation markers. We also validated these selected DNA methylation markers in the replication set. Our results indicate that multiplex DNA methylation markers may be useful for distinguishing patients with MDD from non-psychiatric controls.