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Alterations in cytosine methylation and species-specific transcription induced by interspecific hybridization between Oryza sativa and O. officinalis.

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Interspecific hybridization and polyploidization may involve programmed genetic and epigenetic changes. In this study, we used the methylation-sensitive amplified polymorphism (MSAP) method to survey cytosine methylation alterations that occurred in F(1) hybrid and BC(1) progeny following

Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.).

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Cytosine DNA methylation is a conserved epigenetic regulatory mechanism in both plants and animals. DNA methyltransferases (DNA MTases) not only initiate (de novo) but also maintain the process of DNA methylation. Here, we characterized the genome-wide expression profiles of 10 cytosine DNA MTase

Selective acquisition and retention of genomic sequences by Pack-Mutator-like elements based on guanine-cytosine content and the breadth of expression.

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The process of gene duplication followed by sequence and functional divergence is important for the generation of new genes. Pack-MULEs, nonautonomous Mutator-like elements (MULEs) that carry genic sequence(s), are potentially involved in generating new open reading frames and regulating parental

Cytosine Methylation Affects the Mutability of Neighbouring Nucleotides in Germline and Soma.

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Methylated cytosines deaminate at higher rates than unmethylated cytosines and the lesions they produce are repaired less efficiently. As a result, methylated cytosines are mutational hotspots. Here, combining rare polymorphism and base-resolution methylation data in human, Arabidopsis

Target Specificity of the CRISPR-Cas9 System in Arabidopsis thaliana, Oryza sativa, and Glycine max Genomes.
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Clustered regularly interspaced short palindromic repeats (CRISPR), a class of immune-associated sequences in bacteria, have been developed as a powerful tool for editing eukaryotic genomes in diverse cells and organisms in recent years. The CRISPR-Cas9 system can recognize upstream 20 nucleotides

Cytosine methylations in the promoter regions of genes involved in the cellular oxidation equilibrium pathways affect rice heat tolerance
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Background: High temperatures, particularly at night, decrease rice yield and quality. As high nighttime temperatures (HNTs) become increasingly frequent due to climate change, it is imperative to develop rice crops that tolerate HNTs.

A single cytosine deletion in the OsPLS1 gene encoding vacuolar-type H+-ATPase subunit A1 leads to premature leaf senescence and seed dormancy in rice.
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Leaf senescence is a programmed developmental process orchestrated by many factors, but its molecular regulation is not yet fully understood. In this study, a novel Oryza sativa premature leaf senescence mutant (ospls1) was examined. Despite normal development in early seedlings, the ospls1 mutant

Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa.
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BACKGROUND The methylation of cytosines at CpG dinucleotides, which plays an important role in gene expression regulation, is one of the most studied epigenetic modifications. Thus far, the detection of DNA methylation has been determined mostly by experimental methods, which are not only prone to

Rice cytosine DNA methyltransferases - gene expression profiling during reproductive development and abiotic stress.
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DNA methylation affects important developmental processes in both plants and animals. The process of methylation of cytosines at C-5 is catalysed by DNA methyltransferases (MTases), which are highly conserved, both structurally and functionally, in eukaryotes. In this study, we identified and

Spaceflight-induced genetic and epigenetic changes in the rice (Oryza sativa L.) genome are independent of each other.
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An array of studies have reported that the spaceflight environment is mutagenic and may induce phenotypic and genetic changes in diverse organisms. We reported recently that in at least some plant species (e.g., rice) the spaceflight environment can be particularly potent in generating heritable

Alterations of Rice ( Oryza sativa L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus
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Rice black-streaked dwarf virus (RBSDV) causes severe yield losses in rice (Oryza sativa L.) in China. Studies have shown that the mechanisms of DNA methylation-mediated plant defense against DNA viruses and RNA viruses are different. However, in rice its function in response to infection of

Heritable alteration in DNA methylation induced by nitrogen-deficiency stress accompanies enhanced tolerance by progenies to the stress in rice (Oryza sativa L.).
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Cytosine methylation is responsive to various biotic- and abiotic-stresses, which may produce heritable epialleles. Nitrogen (N)-deficiency is an abiotic stress being repeatedly experienced by plants. To address possible epigenetic consequences of N-deficiency-stress, we investigated the stability

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions.
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Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding

Duplication and diversification of the LEAFY HULL STERILE1 and Oryza sativa MADS5 SEPALLATA lineages in graminoid Poales.
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BACKGROUND Gene duplication and the subsequent divergence in function of the resulting paralogs via subfunctionalization and/or neofunctionalization is hypothesized to have played a major role in the evolution of plant form. The LEAFY HULL STERILE1 (LHS1) SEPALLATA (SEP) genes have been linked with

Genome-wide identification, classification, expression profiling and DNA methylation (5mC) analysis of stress-responsive ZFP transcription factors in rice (Oryza sativa L.).
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Cytosine DNA methylation (5mC) is an epigenetic mark that regulates gene expression in plant responses to environmental stresses. Zinc-finger protein (ZFP) is the largest family of DNA-binding transcription factors that also plays an essential role in eukaryote. In plant we have already identified

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cytosine/ryż siewny

Alterations in cytosine methylation and species-specific transcription induced by interspecific hybridization between Oryza sativa and O. officinalis.

Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.).

Selective acquisition and retention of genomic sequences by Pack-Mutator-like elements based on guanine-cytosine content and the breadth of expression.

Cytosine Methylation Affects the Mutability of Neighbouring Nucleotides in Germline and Soma.

Target Specificity of the CRISPR-Cas9 System in Arabidopsis thaliana, Oryza sativa, and Glycine max Genomes.

Cytosine methylations in the promoter regions of genes involved in the cellular oxidation equilibrium pathways affect rice heat tolerance

A single cytosine deletion in the OsPLS1 gene encoding vacuolar-type H+-ATPase subunit A1 leads to premature leaf senescence and seed dormancy in rice.

Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa.

Rice cytosine DNA methyltransferases - gene expression profiling during reproductive development and abiotic stress.

Spaceflight-induced genetic and epigenetic changes in the rice (Oryza sativa L.) genome are independent of each other.

Alterations of Rice ( Oryza sativa L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus

Heritable alteration in DNA methylation induced by nitrogen-deficiency stress accompanies enhanced tolerance by progenies to the stress in rice (Oryza sativa L.).

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions.

Duplication and diversification of the LEAFY HULL STERILE1 and Oryza sativa MADS5 SEPALLATA lineages in graminoid Poales.

Genome-wide identification, classification, expression profiling and DNA methylation (5mC) analysis of stress-responsive ZFP transcription factors in rice (Oryza sativa L.).

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