Contiguous and stochastic CHH methylation patterns of plant DRM2 and CMT2 revealed by single-read methylome analysis

Harris, Keith D.; Zemach, Assaf

doi:10.1186/s13059-020-02099-9

Cited by 21 publications

(23 citation statements)

References 61 publications

(104 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As said earlier, while vertebrate DNA cytosine methylation is primarily found in the CG context, plants have significant levels of DNA methylation in the CG, CHG and CHH contexts [39, 15]. To focus on CHG and CHH methylation we selected five plant species for which BS-Seq data was available, namely (1) Arabidopsis thaliana representing the Brassicales order, (2) rice ( Oryza sativa ) representing the Paoles order (the only monocotyledons in our study), (3) tomato ( Solanum lycopersicum ) representing the Solanales order, (4) cucumber ( Cucumis sativus ) representing the Cucurbitales order, and (5) cowpea ( Vigna unguiculata ) representing the Fabales order.…”

Section: Resultsmentioning

confidence: 99%

“…In plants and other non-vertebrates, cytosine methylation in the CHH and CHG contexts (where H represents any base except G) is almost as common as methylation in CG context [13, 14]. It is now well-understood that distinct molecular mechanisms in the cells regulate cytosine methylation and demethylation depending on the context [15, 16, 17, 18].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

On the Prediction of non-CG DNA Methylation

Sereshki

Omirou

Fasoula

et al. 2022

Preprint

View full text Add to dashboard Cite

DNA cytosine methylation is an epigenetic modification that has a critical role in gene regulation and genome stability. DNA methylation can be detected and measured using sequencing instruments after sodium bisulfite conversion, but experiments can be expensive for large eukaryotic genomes. Sequencing non-uniformity and mapping biases can leave parts of the genome with low or no coverage, thus hampering the ability of obtaining DNA methylation levels for all cytosines. To address these limitations, several computational methods have been proposed that can predict DNA methylation from the DNA sequence around the cytosine, or from the methylation level of nearby cytosines. Most of these methods are, however, entirely focused on CG methylation in humans and other mammals. In this work, we study for the first time the problem of predicting cytosine methylation for CG, CHG, and CHH contexts on five plant species, either from the DNA primary sequence around the cytosine or the methylation levels of neighboring cytosines. In this framework, we also study (1) the cross-species prediction problem, i.e., the classification performance when training on one species and testing on another species, and the (2) the cross-context prediction problem, i.e., the classification performance when training on one context and testing on another context (within the same species). Finally, we show that providing the classifier with gene annotation information allows our classifier to outperform the prediction accuracy of state-of-the-art methods.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

On the Prediction of non-CG DNA Methylation

Sereshki

Omirou

Fasoula

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Future work is needed to investigate the presence and potential role of CHH islands in almond and their possible functions and impact on NBF potential. CHH methylation is biologically intriguing given that it is independent of demethylase activity and chromatin structure; therefore, its characterization may require additional tools to better understand its dynamics ( Harris and Zemach, 2020 ). Additionally, CHH methylation has been shown to be involved in regulating the expression of transposable elements in plant genomes ( Harris and Zemach, 2020 ; Wang and Baulcombe, 2020 ; Xin et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…CHH methylation is biologically intriguing given that it is independent of demethylase activity and chromatin structure; therefore, its characterization may require additional tools to better understand its dynamics ( Harris and Zemach, 2020 ). Additionally, CHH methylation has been shown to be involved in regulating the expression of transposable elements in plant genomes ( Harris and Zemach, 2020 ; Wang and Baulcombe, 2020 ; Xin et al, 2021 ). Prediction analysis using gene expression data in this study indicates expression of transposable element 1 from both almond and peach are highly predictive of NBF exhibition.…”

Section: Discussionmentioning

confidence: 99%

Identification of Putative Markers of Non-infectious Bud Failure in Almond [Prunus dulcis (Mill.) D.A. Webb] Through Genome Wide DNA Methylation Profiling and Gene Expression Analysis in an Almond × Peach Hybrid Population

et al. 2022

View full text Add to dashboard Cite

Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important nut crop susceptible to the genetic disorder, Non-infectious Bud Failure (NBF). Despite the severity of exhibition in several prominent almond cultivars, no causal mechanism has been identified underlying NBF development. The disorder is hypothesized to be associated with differential DNA methylation patterns based on patterns of inheritance (i.e., via sexual reproduction and clonal propagation) and previous work profiling methylation in affected trees. Peach (Prunus persica L. Batsch) is a closely related species that readily hybridizes with almond; however, peach is not known to exhibit NBF. A cross between an NBF-exhibiting ‘Carmel’ cultivar and early flowering peach (‘40A17’) produced an F1 where ∼50% of progeny showed signs of NBF, including canopy die-back, erratic branching patterns (known as “crazy-top”), and rough bark. In this study, whole-genome DNA methylation profiles were generated for three F1 progenies exhibiting NBF and three progenies considered NBF-free. Subsequent alignment to both the almond and peach reference genomes showed an increase in genome-wide methylation levels in NBF hybrids in CG and CHG contexts compared to no-NBF hybrids when aligned to the almond genome but no difference in methylation levels when aligned to the peach genome. Significantly differentially methylated regions (DMRs) were identified by comparing methylation levels across the genome between NBF- and no-NBF hybrids in each methylation context. In total, 115,635 DMRs were identified based on alignment to the almond reference genome, and 126,800 DMRs were identified based on alignment to the peach reference genome. Nearby genes were identified as associated with the 39 most significant DMRs occurring either in the almond or peach alignments alone or occurring in both the almond and peach alignments. These DMR-associated genes include several uncharacterized proteins and transposable elements. Quantitative PCR was also performed to analyze the gene expression patterns of these identified gene targets to determine patterns of differential expression associated with differential DNA methylation. These DMR-associated genes, particularly those showing corresponding patterns of differential gene expression, represent key targets for almond breeding for future cultivars and mitigating the effects of NBF-exhibition in currently affected cultivars.

show abstract

“…Importantly, a genome-wide decrease in CHH methylation was previously associated with hybrid vigour in Arabidopsis , and correlates with a general decrease of 24 nt siRNAs 29 , 32 . Nonetheless, plant DNA methylation in CHH context is considered to be highly stochastic 33 , and it is, therefore, remarkable to observe that DMRs have been found almost exclusively hypomethylated. However, previous studies performed on epigenetic hybrids showed that only a subset of DMRs can be directly associated with heterosis 31 , and we also found only little overlap among differentially express genes and DMRs in hetero-grafted vigorous scions.…”

Section: Discussionmentioning

confidence: 99%

Grafting vigour is associated with DNA de-methylation in eggplant

et al. 2021

View full text Add to dashboard Cite

In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Rootstocks can provide resistance to stress and increase plant production, but despite their wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown. Given that epigenetics plays a relevant role during distance signalling in plants, we studied the genome-wide DNA methylation changes induced in eggplant (Solanum melongena) scion using two interspecific rootstocks to increase vigour. We found that vigour was associated with a change in scion gene expression and a genome-wide hypomethylation in the CHH context. Interestingly, this hypomethylation correlated with the downregulation of younger and potentially more active long terminal repeat retrotransposable elements (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated with both physiological and molecular phenotypes in grafted plants. Our results indicate that the enhanced vigour induced by heterografting in eggplant is associated with epigenetic modifications, as also observed in some heterotic hybrids.

show abstract

Contiguous and stochastic CHH methylation patterns of plant DRM2 and CMT2 revealed by single-read methylome analysis

Cited by 21 publications

References 61 publications

On the Prediction of non-CG DNA Methylation

On the Prediction of non-CG DNA Methylation

Identification of Putative Markers of Non-infectious Bud Failure in Almond [Prunus dulcis (Mill.) D.A. Webb] Through Genome Wide DNA Methylation Profiling and Gene Expression Analysis in an Almond × Peach Hybrid Population

Grafting vigour is associated with DNA de-methylation in eggplant

Contact Info

Product

Resources

About