scholarly journals Inheritance of DNA Methylation in Plant Genome

10.5772/33904 ◽  
2012 ◽  
Author(s):  
Tomoko Takamiya ◽  
Saeko Hosobuchi ◽  
Kaliyamoorthy Seetharam ◽  
Yasufumi Murakami ◽  
Hisato Okuizumi
Keyword(s):  
Dna Methylation ◽  
Plant Genome

scholarly journals Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley

2021 ◽  
Vol 22 (13) ◽  
pp. 6783
Author(s):  
Renata Orłowska ◽  
Katarzyna A. Pachota ◽  
Wioletta M. Dynkowska ◽  
Agnieszka Niedziela ◽  
Piotr T. Bednarek
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Nuclear Dna ◽  
Point Mutations ◽  
Mobile Elements ◽  
Dna Demethylation ◽  
Plant Genome

A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.

scholarly journals RNA directed DNA methylation and seed plant genome evolution

2020 ◽  
Vol 39 (8) ◽  
pp. 983-996
Author(s):  
R. Wambui Mbichi ◽  
Qing-Feng Wang ◽  
Tao Wan
Keyword(s):  
Dna Methylation ◽  
Genome Evolution ◽  
Plant Genome ◽  
Seed Plant ◽  
Plant Genome Evolution

scholarly journals DNA Methylation Changes and Its Associated Genes in Mulberry (Morus alba L.) Yu-711 Response to Drought Stress Using MethylRAD Sequencing

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 190
Author(s):  
Michael Ackah ◽  
Liangliang Guo ◽  
Shaocong Li ◽  
Xin Jin ◽  
Charles Asakiya ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Regulation ◽  
Drought Stress ◽  
Methylation Status ◽  
Enrichment Analysis ◽  
Plant Genome ◽  
Pcr Analysis ◽  
Kegg Pathways ◽  
Wide Range ◽  
And Control

Drought stress remains one of the most detrimental environmental cues affecting plant growth and survival. In this work, the DNA methylome changes in mulberry leaves under drought stress (EG) and control (CK) and their impact on gene regulation were investigated by MethylRAD sequencing. The results show 138,464 (37.37%) and 56,241 (28.81%) methylation at the CG and CWG sites (W = A or T), respectively, in the mulberry genome between drought stress and control. The distribution of the methylome was prevalent in the intergenic, exonic, intronic and downstream regions of the mulberry plant genome. In addition, we discovered 170 DMGs (129 in CG sites and 41 in CWG sites) and 581 DMS (413 in CG sites and 168 in CWG sites). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicates that phenylpropanoid biosynthesis, spliceosome, amino acid biosynthesis, carbon metabolism, RNA transport, plant hormone, signal transduction pathways, and quorum sensing play a crucial role in mulberry response to drought stress. Furthermore, the qRT-PCR analysis indicates that the selected 23 genes enriched in the KEGG pathways are differentially expressed, and 86.96% of the genes share downregulated methylation and 13.04% share upregulation methylation status, indicating the complex link between DNA methylation and gene regulation. This study serves as fundamentals in discovering the epigenomic status and the pathways that will significantly enhance mulberry breeding for adaptation to a wide range of environments.

scholarly journals DNA methylation mutants in Physcomitrella patens elucidate individual roles of CG and non-CG methylation in genome regulation

2020 ◽  
Vol 117 (52) ◽  
pp. 33700-33710
Author(s):  
Katherine Domb ◽  
Aviva Katz ◽  
Keith D. Harris ◽  
Rafael Yaari ◽  
Efrat Kaisler ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Physcomitrella Patens ◽  
Plant Genome ◽  
Specific Effects ◽  
Genome Regulation ◽  
Expression Of Genes ◽  
The Individual ◽  
Context Specific ◽  
Study Context ◽  
Or Genes

Cytosine (DNA) methylation in plants regulates the expression of genes and transposons. While methylation in plant genomes occurs at CG, CHG, and CHH sequence contexts, the comparative roles of the individual methylation contexts remain elusive. Here, we present Physcomitrella patens as the second plant system, besides Arabidopsis thaliana, with viable mutants with an essentially complete loss of methylation in the CG and non-CG contexts. In contrast to A. thaliana, P. patens has more robust CHH methylation, similar CG and CHG methylation levels, and minimal cross-talk between CG and non-CG methylation, making it possible to study context-specific effects independently. Our data found CHH methylation to act in redundancy with symmetric methylation in silencing transposons and to regulate the expression of CG/CHG-depleted transposons. Specific elimination of CG methylation did not dysregulate transposons or genes. In contrast, exclusive removal of non-CG methylation massively up-regulated transposons and genes. In addition, comparing two exclusively but equally CG- or CHG-methylated genomes, we show that CHG methylation acts as a greater transcriptional regulator than CG methylation. These results disentangle the transcriptional roles of CG and non-CG, as well as symmetric and asymmetric methylation in a plant genome, and point to the crucial role of non-CG methylation in genome regulation.

scholarly journals The Underlying Nature of Epigenetic Variation: Origin, Establishment and Regulatory Function of Plant Epialleles

2021 ◽  
Vol 22 (16) ◽  
pp. 8618
Author(s):  
Thanvi Srikant ◽  
Anjar Tri Wibowo
Keyword(s):  
Dna Methylation ◽  
Genetic Architecture ◽  
Genetic Variations ◽  
Plant Genome ◽  
Regulatory Function ◽  
Dynamic Changes ◽  
Genetic Changes ◽  
Genomic Location ◽  
Adaptive Processes ◽  
Genomic Regions

In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.

scholarly journals Contrasting epigenetic control of transgenes and endogenous genes promotes post-transcriptional transgene silencing in Arabidopsis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicolas Butel ◽  
Agnès Yu ◽  
Ivan Le Masson ◽  
Filipe Borges ◽  
Taline Elmayan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Host Plant ◽  
Transgene Silencing ◽  
Plant Genome ◽  
Plant Genomes ◽  
Epigenetic Control ◽  
Specific Attenuation ◽  
Endogenous Genes ◽  
Chromatin Modifying Complex

AbstractTransgenes that are stably expressed in plant genomes over many generations could be assumed to behave epigenetically the same as endogenous genes. Here, we report that whereas the histone H3K9me2 demethylase IBM1, but not the histone H3K4me3 demethylase JMJ14, counteracts DNA methylation of Arabidopsis endogenous genes, JMJ14, but not IBM1, counteracts DNA methylation of expressed transgenes. Additionally, JMJ14-mediated specific attenuation of transgene DNA methylation enhances the production of aberrant RNAs that readily induce systemic post-transcriptional transgene silencing (PTGS). Thus, the JMJ14 chromatin modifying complex maintains expressed transgenes in a probationary state of susceptibility to PTGS, suggesting that the host plant genome does not immediately accept expressed transgenes as being epigenetically the same as endogenous genes.

scholarly journals Assessment of Epigenetic and Phenotypic Variation in Populus nigra Regenerated via Sequential Regeneration

2021 ◽  
Vol 12 ◽  
Author(s):  
Weixi Zhang ◽  
Yanbo Wang ◽  
Shu Diao ◽  
Shanchen Zhong ◽  
Shu Wu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Phenotypic Variation ◽  
Populus Nigra ◽  
Utilization Efficiency ◽  
Plant Genome ◽  
Physiological Traits ◽  
Somatic Variation ◽  
Regenerated Plants ◽  
Significant Difference ◽  
Almost All

Somatic variation has been demonstrated in tissue culture regenerated plants of many species. In the genus Populus, phenotypic variation caused by changes in 5-methylcytosine within the plant genome have been reported. To date, the phenotypic and epigenetic stability of plants regenerated from sequential regeneration has not been tested in trees. In this study, we detected DNA methylation of CCGG sites in regenerated plants of five generations in Populus nigra using methylation-sensitive amplified polymorphisms, and evaluated their growth performance and physiological traits. About 10.86–26.80% of CCGG sites in the regenerated plant genome were demethylated and 5.50–8.45% were methylated, resulting in significantly lower DNA methylation levels among all regenerated plants than among donor plants. We detected a significant difference in methylation levels between first regeneration regenerated plants (G1) and those of the other four generations (G2–G5); there were no significant differences among the four later generations. Therefore, the dramatic decrease in DNA methylation levels occurred only in the first and second poplar regenerations; levels then stabilized later in the regeneration process, indicating that two regeneration events were sufficient to change the methylation statuses of almost all CCGG sites sensitive to regeneration. Differences in growth and physiological traits were observed between regenerated plants and donor plants, but were significant only among plants of certain generations. Significant correlations were detected between methylation level and transpiration rate, net photosynthetic rate, peroxidase activity, and instant water utilization efficiency, indicating the involvement of epigenetic regulation in this unpredictable phenotypic variation.

scholarly journals A new role for histone demethylases in the maintenance of plant genome integrity

2020 ◽  
Author(s):  
Javier Antunez-Sanchez ◽  
Matthew Naish ◽  
Juan Sebastian Ramirez-Prado ◽  
Sho Ohno ◽  
Ying Huang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Sexual Reproduction ◽  
Critical Role ◽  
Early Flowering ◽  
Plant Genome ◽  
Genome Integrity ◽  
Histone Demethylases ◽  
Genomic Distribution ◽  
Polycomb Repressive Complex 2 ◽  
Growth Development

AbstractHistone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development and adaptation to environmental fluctuations in most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K27me3. Here, we show that two JMJ histone demethylases in Arabidopsis, EARLY FLOWERING 6 (ELF6) and RELATIVE OF EARLY FLOWERING 6 (REF6), play distinct roles in H3K27me3 and H3K27me1 homeostasis. We show that failure to reset these chromatin marks during sexual reproduction results in the inheritance of epigenetic imprints, which cause a loss of DNA methylation at heterochromatic loci and transposon activation. Thus, Jumonji-type histone demethylases in plants contribute towards maintaining distinct transcriptional states during development and help safeguard genome integrity following sexual reproduction.

scholarly journals The complex architecture of plant transgene insertions

2018 ◽  
Author(s):  
Florian Jupe ◽  
Todd P. Michael ◽  
Angeline C. Rivkin ◽  
Mark Zander ◽  
S. Timothy Motley ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Molecule ◽  
Large Scale ◽  
Genome Engineering ◽  
De Novo ◽  
Plant Genome ◽  
Nanopore Sequencing ◽  
Dna Arrays ◽  
In Planta ◽  
Actual Length

AbstractOver the last 35 years the soil bacterium Agrobacterium tumefaciens has been the workhorse tool for plant genome engineering. Replacement of native tumor-inducing (Ti) plasmid elements with customizable cassettes enabled insertion of a sequence of interest called Transfer DNA (T-DNA) into any plant genome. Although these T-DNA transfer mechanisms are well understood, detailed understanding of structure and epigenomic status of insertion events was limited by current technologies. To fill this gap, we analyzed transgenic Arabidopsis thaliana lines from three widely used collections (SALK, SAIL and WISC) with two single molecule technologies, optical genome mapping and nanopore sequencing. Optical maps for four randomly selected T-DNA lines revealed between one and seven insertions/rearrangements, and for the first time the actual length of individual transgene insertions from 27 to 236 kilobases. De novo nanopore sequencing-based genome assemblies for two segregating lines resolved T-DNA structures up to 36 kb into the insertions and revealed large-scale T-DNA associated translocations and exchange of chromosome arm ends. The multiple internally rearranged nature of T-DNA arrays made full assembly impossible, even with long nanopore reads. For the current TAIR10 reference genome, nanopore contigs corrected 83% of non-centromeric misassemblies. This unprecedented nucleotide-level definition of T-DNA insertions enabled the mapping of epigenome data. We identify variable small RNA transgene targeting and DNA methylation. SALK_059379 T-DNA insertions were enriched for 24nt siRNAs and contained dense cytosine DNA methylation. Transgene silencing via the RNA-directed DNA methylation pathway was confirmed by in planta assays. In contrast, SAIL_232 T-DNA insertions are predominantly targeted by 21/22nt siRNAs, with DNA methylation and silencing limited to a reporter, but not the resistance gene. With the emergence of genome editing technologies that rely on Agrobacterium for gene delivery, this study provides new insights into the structural impact of engineering plant genomes and demonstrates the utility of state-of-the-art long-range sequencing technologies to rapidly identify unanticipated genomic changes.

scholarly journals Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis transposons and gene regulatory regions

2017 ◽  
Author(s):  
Kyuha Choi ◽  
Xiaohui Zhao ◽  
Christophe Lambing ◽  
Charles J. Underwood ◽  
Thomas J. Hardcastle ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Genome Instability ◽  
Nucleosome Occupancy ◽  
Plant Genome ◽  
Gene Promoters ◽  
Regulatory Regions ◽  
Plant Genomes ◽  
Meiotic Dsbs ◽  
Gene Regulatory

AbstractMeiotic recombination initiates via DNA double strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Recombination frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis SPO11-1-oligonucleotides. DSB hotspots occurred in gene promoters, terminators and introns, driven by AT-sequence richness, which excludes nucleosomes and allows SPO11-1 access. A strong positive relationship was observed between SPO11-1 DSBs and final crossover levels. Euchromatic marks promote recombination in fungi and mammals, and consistently we observe H3K4me3 enrichment in proximity to DSB hotspots at gene 5’-ends. Repetitive transposons are thought to be recombination-silenced during meiosis, in order to prevent non-allelic interactions and genome instability. Unexpectedly, we found strong DSB hotspots in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. Hotspot transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination-enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin on the DSB landscape. Epigenetic activation of transposon meiotic DSBs occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription and H3K4me3. Increased met1 SPO11-1 DSBs occurred most strongly within centromeres and Gypsy and CACTA/EnSpm coldspot transposons. Together, our work reveals complex interactions between chromatin and meiotic DSBs within genes and transposons, with significance for the diversity and evolution of plant genomes.

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