Whole‐genome DNA methylation patterns of <scp><i>Oryza sativa</i></scp> (L.) and <i>Oryza glumaepatula</i> (Steud) genotypes associated with aluminum response

Gallo-Franco, Jenny Johana; Ghneim-Herrera, Thaura; Tobar-Tosse, Fabián; Romero, Miguel; Chaura, Juliana; Quimbaya, Mauricio

doi:10.1002/pld3.430

Cited by 6 publications

(5 citation statements)

References 59 publications

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“…This is a consequence of low CHH methylation near the centromere region and greater presence in the chromosome arms. Gallo-Franco et al [ 27 ] reported high CHH methylation levels of transposable elements close to genes in rice, which supports the conclusion of Martin et al [ 28 ] for grass species that long genes and genes close to transposable elements tend to have CHH islands more frequently. It could be hypothesized that the presence of these CHH islands is promoting the positive correlation between methylation and recombination in gene-rich regions.…”

Section: Resultssupporting

confidence: 64%

Methylation in the CHH Context Allows to Predict Recombination in Rice

Peñuela

Gallo-Franco

Finke

et al. 2022

IJMS

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DNA methylation is the most studied epigenetic trait. It is considered a key factor in regulating plant development and physiology, and has been associated with the regulation of several genomic features, including transposon silencing, regulation of gene expression, and recombination rates. Nonetheless, understanding the relation between DNA methylation and recombination rates remains a challenge. This work explores the association between recombination rates and DNA methylation for two commercial rice varieties. The results show negative correlations between recombination rates and methylated cytosine counts for all contexts tested at the same time, and for CG and CHG contexts independently. In contrast, a positive correlation between recombination rates and methylated cytosine count is reported in CHH contexts. Similar behavior is observed when considering only methylated cytosines within genes, transposons, and retrotransposons. Moreover, it is shown that the centromere region strongly affects the relationship between recombination rates and methylation. Finally, machine learning regression models are applied to predict recombination using the count of methylated cytosines in the CHH context as the entrance feature. These findings shed light on the understanding of the recombination landscape of rice and represent a reference framework for future studies in rice breeding, genetics, and epigenetics.

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Section: Resultssupporting

confidence: 64%

Methylation in the CHH Context Allows to Predict Recombination in Rice

Peñuela

Gallo-Franco

Finke

et al. 2022

IJMS

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“…CHH was the context with least negative correlation of genes to methylation for Acer. Less correlation of methylation with genes means more intersection in TE filled intergenic space, lending support to the hypothesis that in some species, the balance of CHH methylation, TE suppression, TE proximity to genes, and gene body methylation could indicate complex strategies playing a role regulating key genes at TE boundary regions, as observed in grasses(Martin et al, 2021) and Oryza(Gallo-Franco et al, 2022).…”

supporting

confidence: 64%

“…Gallo‐Franco et al. ( 2022 ) found that aluminum tolerant and susceptible varieties of O. sativa and Oryza glumaepatula each had unique differentially methylated regions, and each species was associated with different TEs potentially affecting regulation of these regions. While relationships between environmental stress, methylation, and increased proximal TE activity have been observed in numerous studies, this regulation is complex and potentially involves specific methylation mechanisms, such as the Copia ONSEN in both Arabidopsis and Oryza .…”

Section: Resultsmentioning

confidence: 99%

Profiling genome‐wide methylation in two maples: Fine‐scale approaches to detection with nanopore technology

McEvoy,

Grady,

Pauloski

et al. 2024

Evolutionary Applications

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DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long‐read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long‐reads. Hybrid and reference‐guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re‐basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.

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“…In rice, a genome-wide methylation comparison between cultivated ( Oryza sativa ) and the more Al tolerant wild species ( O. glumaepatula ) was undertaken ( Gallo-Franco et al., 2022 ). In the case of O. sativa , 4633 differentially methylated regions (DMRs) were observed - 38% showed increased methylation and 62% were hypomethylated.…”

Section: Dna Methylationmentioning

confidence: 99%

“…Lastly, DNA as well as RNA methylation leads to the regulation of the expression of stress signalling and defense associated genes. The WGBS analysis revealed thousands of differentially methylated regions in plants in response to Cd, Pb, Al and Hg treatment ( Cong et al., 2021 , Feng et al., 2016 ; Gallo-Franco et al., 2022 ; Tang et al., 2023 ). In rice, the majority (nearly 70%) of Cd responsive genes were also differentially methylated.…”

Section: The Relation Of Epigenetic and Epitranscriptomic Changes To ...mentioning

confidence: 99%

The role of epigenetic and epitranscriptomic modifications in plants exposed to non-essential metals

Chmielowska-Bąk,

Searle,

Wakai

et al. 2023

Front. Plant Sci.

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Contamination of the soil with non-essential metals and metalloids is a serious problem in many regions of the world. These non-essential metals and metalloids are toxic to all organisms impacting crop yields and human health. Crop plants exposed to high concentrations of these metals leads to perturbed mineral homeostasis, decreased photosynthesis efficiency, inhibited cell division, oxidative stress, genotoxic effects and subsequently hampered growth. Plants can activate epigenetic and epitranscriptomic mechanisms to maintain cellular and organism homeostasis. Epigenetic modifications include changes in the patterns of cytosine and adenine DNA base modifications, changes in cellular non-coding RNAs, and remodeling histone variants and covalent histone tail modifications. Some of these epigenetic changes have been shown to be long-lasting and may therefore contribute to stress memory and modulated stress tolerance in the progeny. In the emerging field of epitranscriptomics, defined as chemical, covalent modifications of ribonucleotides in cellular transcripts, epitranscriptomic modifications are postulated as more rapid modulators of gene expression. Although significant progress has been made in understanding the plant’s epigenetic changes in response to biotic and abiotic stresses, a comprehensive review of the plant’s epigenetic responses to metals is lacking. While the role of epitranscriptomics during plant developmental processes and stress responses are emerging, epitranscriptomic modifications in response to metals has not been reviewed. This article describes the impact of non-essential metals and metalloids (Cd, Pb, Hg, Al and As) on global and site-specific DNA methylation, histone tail modifications and epitranscriptomic modifications in plants.

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Whole‐genome DNA methylation patterns of Oryza sativa (L.) and Oryza glumaepatula (Steud) genotypes associated with aluminum response

Cited by 6 publications

References 59 publications

Methylation in the CHH Context Allows to Predict Recombination in Rice

Methylation in the CHH Context Allows to Predict Recombination in Rice

Profiling genome‐wide methylation in two maples: Fine‐scale approaches to detection with nanopore technology

The role of epigenetic and epitranscriptomic modifications in plants exposed to non-essential metals

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