AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Shahryary, Yadollah; Symeonidi, Aikaterini; Hazarika, Rashmi R.; Denkena, Johanna; Mubeen, Talha; Hofmeister, Brigitte T.; Gurp, Thomas van; Colomé-Tatché, Maria; Verhoeven, Koen; Tuskan, Gerald A.; Schmitz, Robert J.; Johannes, Frank

doi:10.1186/s13059-020-02161-6

Cited by 37 publications

(30 citation statements)

References 64 publications

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“…Spontaneous or random errors in the maintenance of methylation lead to ‘epimutation’ and generate single methylation polymorphisms (SMPs) including CG-, CHG-, CHH-SMPs [ 91 ], or differentially methylated regions (DMRs) [ 92 ]. Spontaneous epimutation rates are estimated to be similar across species [ 93 ], with SMPs in the range 1 × 10 −4 to 10 −5 sites/haploid/generation, which is far higher than SNPs (1 × 10 −8 to 10 −9 ) [ 86 ]. In contrast with SMPs, the level of methylation across larger regions is more stable (1 × 10 −5 to 10 −6 sites/haploid/generation) [ 94 , 95 ].…”

Section: Opportunities and Challenges For Crop Improvementmentioning

confidence: 99%

Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits

Vafadarshamasbi

Mace

Jordan

et al. 2022

Biochemical Society Transactions

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DNA methylation is a chromatin modification that plays an essential role in regulating gene expression and genome stability and it is typically associated with gene silencing and heterochromatin. Owing to its heritability, alterations in the patterns of DNA methylation have the potential to provide for epigenetic inheritance of traits. Contemporary epigenomic technologies provide information beyond sequence variation and could supply alternative sources of trait variation for improvement in crops such as sorghum. Yet, compared with other species such as maize and rice, the sorghum DNA methylome is far less well understood. The distribution of CG, CHG, and CHH methylation in the genome is different compared with other species. CG and CHG methylation levels peak around centromeric segments in the sorghum genome and are far more depleted in the gene dense chromosome arms. The genes regulating DNA methylation in sorghum are also yet to be functionally characterised; better understanding of their identity and functional analysis of DNA methylation machinery mutants in diverse genotypes will be important to better characterise the sorghum methylome. Here, we catalogue homologous genes encoding methylation regulatory enzymes in sorghum based on genes in Arabidopsis, maize, and rice. Discovering variation in the methylome may uncover epialleles that provide extra information to explain trait variation and has the potential to be applied in epigenome-wide association studies or genomic prediction. DNA methylation can also improve genome annotations and discover regulatory elements underlying traits. Thus, improving our knowledge of the sorghum methylome can enhance our understanding of the molecular basis of traits and may be useful to improve sorghum performance.

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Section: Opportunities and Challenges For Crop Improvementmentioning

confidence: 99%

Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits

Vafadarshamasbi

Mace

Jordan

et al. 2022

Biochemical Society Transactions

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“…The WGBS data from the ddm1- epiRILs was analyzed using the Methylstar v1.4 pipeline 75 . Region-level methylation calls were obtained with Methimpute v1.16.0 (200 bp bins, step size = 50 bps, at least 10 cytosines per bin) 76 .…”

Section: Methodsmentioning

confidence: 99%

Heterochromatin is a quantitative trait associated with spontaneous epiallele formation

et al. 2021

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Epialleles are meiotically heritable variations in expression states that are independent from changes in DNA sequence. Although they are common in plant genomes, their molecular origins are unknown. Here we show, using mutant and experimental populations, that epialleles in Arabidopsis thaliana that result from ectopic hypermethylation are due to feedback regulation of pathways that primarily function to maintain DNA methylation at heterochromatin. Perturbations to maintenance of heterochromatin methylation leads to feedback regulation of DNA methylation in genes. Using single base resolution methylomes from epigenetic recombinant inbred lines (epiRIL), we show that epiallelic variation is abundant in euchromatin, yet, associates with QTL primarily in heterochromatin regions. Mapping three-dimensional chromatin contacts shows that genes that are hotspots for ectopic hypermethylation have increases in contact frequencies with regions possessing H3K9me2. Altogether, these data show that feedback regulation of pathways that have evolved to maintain heterochromatin silencing leads to the origins of spontaneous hypermethylated epialleles.

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“…DNA methylation patterns can change either because of failure in maintaining methylation after replication or because of active removal by enzymes (Zhang et al 2018 ). In A. thaliana , it has been reported that CG “germline” epimutations are about five orders of magnitude more frequent than genetic mutations: about 10 −4 vs about 10 −9 per site per haploid genome per generation (Shahryary et al 2020 ).…”

Section: Tools For the Analysis And Characterization Of Cwr Epigeneti...mentioning

confidence: 99%

Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation

et al. 2022

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Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.

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AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Cited by 37 publications

References 64 publications

Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits

Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits

Heterochromatin is a quantitative trait associated with spontaneous epiallele formation

Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation

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