A Non-Rogue Mutant Line Induced by ENU Mutagenesis in Paramutated Rogue Peas (Pisum sativum L.) Is Still Sensitive to the Rogue Paramutation

The spontaneously emerging rogue phenotype in peas (Pisum sativum L.), characterized by narrow and pointed leaf stipula and leaflets, was the first identified case of the epigenetic phenomenon paramutation. The crosses of homozygous or heterozygous (e.g., F1) rogue plants with non-rogue (wild type) plants, produce exclusively rogue plants in the first and all subsequent generations. The fact that the wild phenotype disappears forever, is in clear contradiction with the Mendelian rules of inheritance, a situation that impedes the positional cloning of genes involved in this epigenetic phenomenon. One way of overcoming this obstacle is the identification of plant genotypes harboring naturally occurring or artificially induced neutral alleles, non-sensitive to paramutation. So far, such alleles have never been described for the pea rogue paramutation. Here, we report the induction via 1-ethyl-1-nitrosourea (ENU) mutagenesis of a non-rogue revertant mutant in the rogue cv. Progreta, and the completely unusual fixation of the induced non-rogue phenotype through several generations. The reversion of the methylation status of two previously identified differentially methylated genomic sequences in the induced non-rogue mutant, confirms that the rogue paramutation is accompanied by alterations in DNA methylation. Nevertheless, unexpectedly, the induced non-rogue mutant showed to be still sensitive to paramutation.

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Growth, seed development and genetic analysis in wild type and Def mutant of Pisum sativum L

BMC Research Notes ◽

10.1186/1756-0500-4-489 ◽

2011 ◽

Vol 4 (1) ◽

pp. 489 ◽

Cited By ~ 4

Author(s):

Kwadwo Ayeh ◽

YeonKyeong Lee ◽

Mike J Ambrose ◽

Anne Hvoslef-Eide

Keyword(s):

Pisum Sativum ◽

Genetic Analysis ◽

Seed Development ◽

Wild Type ◽

Pisum Sativum L

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The influence of mitochondria in epigenetics revealed through naturally occurring fish cybrids

Current Zoology ◽

10.1093/czoolo/58.1.138 ◽

2012 ◽

Vol 58 (1) ◽

pp. 138-145 ◽

Cited By ~ 4

Author(s):

Bernard Angers ◽

Antoine Dallaire ◽

Simon Vervaet ◽

Francis Vallières ◽

Annie Angers

Keyword(s):

Dna Methylation ◽

Strong Influence ◽

Nuclear Genome ◽

Genome Comparison ◽

Mitochondrial Genomes ◽

Wild Type ◽

Ideal Model ◽

Naturally Occurring ◽

Cytoplasmic Hybrids ◽

Epigenetic Processes

Abstract Epigenetic processes are important mechanisms for phenotypic changes that occur in response to the environment. As such, it is expected that the alteration of cytoplasmic composition (the immediate environment of nuclei) results in the modification of the methylome and the expression of the nuclear genome. Cytoplasmic hybrids (or cybrids) are an ideal model to study the influence of mitochondria on gene expression. In this study, we take advantage of the natural co-occurrence of two biotypes that have a similar nuclear genome type Chrosomus eos, but harbor mitochondria from different species (C. eos in wild type or C. neogaeus in cybrids) to assess the effects of mitochondria on DNA methylation profiles and protein expression of the nuclear genome. Comparison between these biotypes is particularly relevant given their recent divergence and their low level of genetic differentiation. Variations of DNA methylation assessed on tissues from different embryonic origins revealed the distinct profiles of cybrid and wild type populations. Differences are more pronounced between wild type and cybrids than between populations of a given biotype. The proteome is also more different between biotypes than within a given biotype. These results indicate a strong influence of mitochondria on the nuclear genome, which remains detectable in different genetic and environmental contexts. These changes in the methylome and proteome of cybrids are expected to reflect the adjustments imposed by the coexistence of nuclear and mitochondrial genomes from different species.

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Regulation of the Later Stages of Nodulation Stimulated by IPD3/CYCLOPS Transcription Factor and Cytokinin in Pea Pisum sativum L.

Plants ◽

10.3390/plants11010056 ◽

2021 ◽

Vol 11 (1) ◽

pp. 56

Author(s):

Elizaveta S. Rudaya ◽

Polina Yu. Kozyulina ◽

Olga A. Pavlova ◽

Alexandra V. Dolgikh ◽

Alexandra N. Ivanova ◽

...

Keyword(s):

Transcription Factor ◽

Comparative Analysis ◽

Pisum Sativum ◽

Nodule Development ◽

Rna Seq ◽

Wild Type ◽

Development Stages ◽

Pisum Sativum L ◽

Pea Mutant

The IPD3/CYCLOPS transcription factor was shown to be involved in the regulation of nodule primordia development and subsequent stages of nodule differentiation. In contrast to early stages, the stages related to nodule differentiation remain less studied. Recently, we have shown that the accumulation of cytokinin at later stages may significantly impact nodule development. This conclusion was based on a comparative analysis of cytokinin localization between pea wild type and ipd3/cyclops mutants. However, the role of cytokinin at these later stages of nodulation is still far from understood. To determine a set of genes involved in the regulation of later stages of nodule development connected with infection progress, intracellular accommodation, as well as plant tissue and bacteroid differentiation, the RNA-seq analysis of pea mutant SGEFix--2 (sym33) nodules impaired in these processes compared to wild type SGE nodules was performed. To verify cytokinin’s influence on late nodule development stages, the comparative RNA-seq analysis of SGEFix--2 (sym33) mutant plants treated with cytokinin was also conducted. Findings suggest a significant role of cytokinin in the regulation of later stages of nodule development.

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Organization of the endoplasmic reticulum in cells of effective and ineffective pea nodules (Pisum sativum L.)

Ecological genetics ◽

10.17816/ecogen1745-14 ◽

2019 ◽

Vol 17 (4) ◽

pp. 5-14

Author(s):

Anna V. Tsyganova ◽

Viktor E. Tsyganov

Keyword(s):

Endoplasmic Reticulum ◽

Pisum Sativum ◽

Structural Changes ◽

Nodule Development ◽

Wild Type ◽

Meristematic Cells ◽

Pisum Sativum L ◽

Transmission Electron ◽

Infected Cells ◽

Membrane Bound

Background. The endoplasmic reticulum (ER) is the largest membrane-bound organelle, which plays an important role in the functioning of a plant cell and participates in its differentiation. Materials and methods. Using the methods of transmission electron microscopy, the morphological features and dynamics of structural changes in the ER in symbiotic nodules of pea (Pisum sativum L.) wild-type and mutants blocked at different stages of nodule development were studied. Results. ER developed from a network of individual tubules in meristematic cells, to a developed network of cisterns around the nucleus and plasmalemma, and a network of granular and smooth tubules accompanying infection structures in colonized and infected cells and symbiosomes in infected cells. Conclusions. A correlation was found between the level of development of the ER network and the degree of bacteroid differentiation.

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Characterization and structural analysis of wild type and a non-abscission mutant at the development funiculus (Def) locus in Pisum sativum L

BMC Plant Biology ◽

10.1186/1471-2229-9-76 ◽

2009 ◽

Vol 9 (1) ◽

pp. 76 ◽

Cited By ~ 4

Author(s):

Kwadwo Ayeh ◽

YeonKyeong Lee ◽

Mike J Ambrose ◽

Anne Hvoslef-Eide

Keyword(s):

Structural Analysis ◽

Pisum Sativum ◽

Wild Type ◽

Pisum Sativum L

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DNA Methylation Changes in Plasma Cell Discrasias.

Blood ◽

10.1182/blood.v106.11.1560.1560 ◽

2005 ◽

Vol 106 (11) ◽

pp. 1560-1560

Author(s):

Paloma Martin-Acosta ◽

Dolores Sanchez-Massa ◽

Cesareo Corbacho ◽

Carlos Montalban ◽

Carmen Bellas

Keyword(s):

Dna Methylation ◽

Protein Expression ◽

Gene Silencing ◽

Plasma Cell ◽

Methylation Status ◽

Aberrant Methylation ◽

Gene Methylation ◽

Plasma Cell Disorders ◽

Epigenetic Phenomenon ◽

Methylation Profiling

Abstract Introduction: Aberrant methylation of the 5′ gene promoter regions is an epigenetic phenomenon that is the one of the major mechanism of inactivation of tumor supressor genes. DNA methylation of the promoter region has been described for several genes in various malignant diseases, and each tumour type may have its own pattern of methylation. To determine the methylation status and expression of cell cycle inhibitors genes (p14, p15, p16), repair genes (MGMT and hMLH1) and the apoptosis regulator gene (DAPKinase) and the possible role of this epigenetic phenomenon in tumour progression of plasma cell disorders, we analyzed the methylation profile of MM, MGUS, and plasmacytomas comparing them with their protein expression. Patients and Methods: A total of 51 cases: 30 MM, 13 MGUS, and 8 plasmacytomas (3 Solitary Bone Plasmacytoma, 5 Extramedullary Plasmacytoma) were included in the study. Bone marrow plasma cells were purified using magnetic microbeads labeled with CD138 in samples with MM and MGUS. Methylation-specific polymerase chain reaction (MSP) for p14, p15, p16, MGMT, hMLH1 and DAPKinase was performed. MSP results were matched to protein expression studies by immunohistochemistry for p15, p16, MGMT and hMLH1. Results: The frequency of aberrant methylation among the MM samples was: 50% for p16, 16.7% for p15, 10% for hMLH1, 23.3% for MGMT, 30% for DAPK. In MGUS samples we found 38.5% for p16, 15.4% for p15, 0% for hMLH1, 7.7% for MGMT and 15.4% for DAPK methylation. The frequency of methylation in plasmacytomas was 62.5% for p16, 25% for p15, 0% for hMLH1, 62.5% for MGMT and 50% for DAPK. p14 was unmethylated in all cases (n=51). The correlation between gene methylation status and protein expression was assessed in 17 MM, 11 MGUS, and 8 plasmacytomas and we found that promoter methylation was strongly associated with gene silencing. All the samples methylated had lost the protein expression. In summary these findings demonstrate that aberrant methylation is an important mechanism of gene silencing in plasma cell disorders: 83.3% of MM, 46.1 of MGUS, and 75% of plasmacytomas have at least one hypermethylated gene (figure 1). We also show, that hypermethylation of p16 is a common phenomenon in plasma cell discrasias while there was no methylation of p14. Although the size of sample is small, we found that hMLH1 hypermethylation was found only in MM, while in plasmacytomas hypermethylation of MGMT and DAPK were frequent events. Moreover in survival studies of MM patients, a trend was observed between simultaneous aberrant methylation of hMLH1 and MGMT and poorer survival, but the number of cases studied limits the statistical analysis and the clinical implications of these results. To better define the clinical impact of methylation markers in plasma cell discrasias, it is therefore necessary to analyze a large number of patient samples. Figure 1. Gene methylation profiling of MM(A), MGUS(B), and plasmacytomas(C) using MSPCR Figure 1. Gene methylation profiling of MM(A), MGUS(B), and plasmacytomas(C) using MSPCR

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DNMT3A Mutations Are Connected with Lower DNA Methylation Levels and Numbers of Concurrently Hypermethylated Genes in AML Patients

Blood ◽

10.1182/blood.v118.21.4629.4629 ◽

2011 ◽

Vol 118 (21) ◽

pp. 4629-4629 ◽

Cited By ~ 2

Author(s):

Hana Hajkova ◽

Jana Markova ◽

Cedrik Haskovec ◽

Jaroslav Cermak ◽

Radka Petrbokova ◽

...

Keyword(s):

Dna Methylation ◽

Tumor Suppressor ◽

Tumor Suppressor Genes ◽

Healthy Donor ◽

Hox Genes ◽

Methylation Status ◽

Wild Type ◽

Suppressor Genes ◽

The Impact ◽

Hypermethylated Genes

Abstract Abstract 4629 Recently, mutations in DNA methyltransferase 3A (DNMT3A) have been found in patients with acute myeloid leukemia (AML) and have been confirmed to be connected with adverse clinical outcome. As DNMT3A plays direct role in the process of DNA methylation by adding methyl group to the cytosine residue of CpG dinucleotides, the question is obvious: What is the impact of DNMT3A mutations on DNA methylation levels? We examined 79 AML patients at diagnosis for the presence of aberrant DNA methylation of 12 tumor suppressor genes (TSG) (CDKN2B, CALCA, CDH1, ESR1, SOCS1, MYOD1, DAPK1, TIMP3, ICAM1, TERT, CTNNA1, EGR1) by methylation specific real-time PCR (MethyLight) and for mutations in the gene DNMT3A by direct sequencing. Next we studied methylation status of 24 HOX genes from all four clusters A-D using methylation-restriction endonucleases followed by RQ-PCR arrays in 10 AML samples compared to 4 healthy donor samples. Sequencing of cDNA between amino acids 300 and 930 revealed that 32 of 79 AML patients had DNMT3A mutation. The reason for higher DNMT3A mutation incidence in our patients’ cohort consists in preferential selection of AML patients with a higher percentage of probability of DNMT3A mutation (it means normal karyotype and mutations in NPM1, FLT3 and/or IDH1/2 genes). MethyLight assessment of 12 TSG showed subsequent frequencies of hypermethylation: CDKN2B (47%), CALCA (43%), CDH1 (22%), SOCS1 (24%), MYOD1 (18%), ESR1 (14%). The remaining 6 genes were weakly methylated in less than 10 % AML patients at diagnosis and were therefore excluded from further analysis. DNA methylation arrays revealed a set of differentially methylated HOX genes (n=12): 11 HOX genes were hypermethylated (HOXA4, HOXA6, HOXB13, HOXB3, HOXB4, HOXB7, HOXB8, HOXC8, HOXD10, HOXD11, HOXD3) and HOXA5 was hypomethylated compared to healthy donor samples. Comparing overall cumulative DNA methylation levels and numbers of simultaneously hypermethylated genes to mutational status of DNMT3A gene, we did observe lower levels of DNA methylation (P<0.0001) as well as displaying lower numbers of concurrently hypermethylated genes (P<0.0001) in patients with DNMT3a mutations. We observed the same trend also in DNA methylation levels of HOX genes when compared mutant (n=4) versus wild-type (n=6) DNMT3A patients. These results clearly show that numbers of simultaneously hypermethylated genes and DNA methylation levels of chosen tumor suppressor genes (TSG) as well as HOX genes differs between AML patients with wild type and mutant DNMT3A. This study is part of the COST Action BM0801 (EuGESMA) and is supported by NS10632-3/2009, OC10042 and IHBT00023736. Disclosures: No relevant conflicts of interest to declare.

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Meiotically and Mitotically Stable Inheritance of DNA Hypomethylation Induced by ddm1 Mutation of Arabidopsis thaliana

Genetics ◽

10.1093/genetics/151.2.831 ◽

1999 ◽

Vol 151 (2) ◽

pp. 831-838 ◽

Cited By ~ 6

Author(s):

Tetsuji Kakutani ◽

Kyoko Munakata ◽

Eric J Richards ◽

Hirohiko Hirochika

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Arabidopsis Thaliana ◽

Methylation Status ◽

Wild Type ◽

Dna Hypomethylation ◽

Developmental Abnormalities ◽

Plant Genes ◽

Outcross Progeny ◽

Stable Transmission

Abstract In contrast to mammalian epigenetic phenomena, where resetting of gene expression generally occurs in each generation, epigenetic states of plant genes are often stably transmitted through generations. The Arabidopsis mutation ddm1 causes a 70% reduction in genomic 5-methylcytosine level. We have previously shown that the ddm1 mutation results in an accumulation of a variety of developmental abnormalities by slowly inducing heritable changes in other loci. Each of the examined ddm1-induced developmental abnormalities is stably transmitted even when segregated from the potentiating ddm1 mutation. Here, the inheritance of DNA hypomethylation induced by ddm1 was examined in outcross progeny by HPLC and Southern analyses. The results indicate that (i) DDM1 gene function is not necessary during the gametophyte stage, (ii) ddm1 mutation is completely recessive, and (iii) remethylation of sequences hypomethylated by the ddm1 mutation is extremely slow or nonexistent even in wild-type DDM1 backgrounds. The stable transmission of DNA methylation status may be related to the meiotic heritability of the ddm1-induced developmental abnormalities.

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