DNA methylation profiles of diverse <i>Brachypodium distachyon</i> align with underlying genetic diversity

Eichten, Steven R.; Stuart, T.A.; Srivastava, Akanksha; Lister, Ryan; Borevitz, Justin O.

doi:10.1101/gr.205468.116

Cited by 37 publications

(35 citation statements)

References 74 publications

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“…The average percentages of methylation of CG, CHG and CHH contexts in leaf were 89.7%, 59.1% and 2.1%, respectively (Supplementary Table 24). The genome CG and CHG methylation levels are about the same as those in maize (86.4%, 70.9%) 33 , and are much higher than those in B. distachyon (56.5%, 35.3%) 34 and rice (44%, 24%) 35 . This is consistent with previous observations indicating a positive correlation between genome size, TE content and genomic methylation levels 36 .…”

Section: −13mentioning

confidence: 63%

The Aegilops tauschii genome reveals multiple impacts of transposons

Zhao¹,

Zou²,

et al. 2017

Nature Plants

173

112

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Wheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes. In addition to the discovery of a wave of very recent gene duplications, we detected that TEs occurred in about half of the genes, and found that such genes are expressed at lower levels than those without TEs, presumably because of their elevated methylation levels. We mapped all wheat molecular markers and constructed a high-resolution integrated genetic map corresponding to genome sequences, thereby placing previously detected agronomically important genes/ quantitative trait loci (QTLs) on the Ae. tauschii genome for the first time. NaTuRe PLaNTs

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Section: −13mentioning

confidence: 63%

The Aegilops tauschii genome reveals multiple impacts of transposons

Zhao¹,

Zou²,

et al. 2017

Nature Plants

173

112

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“…Two unbiased approaches were used to identify differentially methylated regions (DMRs) based on previous approaches (Eichten, Stuart, Srivastava, Lister, & Borevitz, ).…”

Section: Methodsmentioning

confidence: 99%

“…The proportion of mCG, mCHG, and mCHH was determined as weighted methylation across reads at single cytosine resolution and across 100 bp tiles for genome-wide comparisons. .7 | Identifying differentially methylated regions Two unbiased approaches were used to identify differentially methylated regions (DMRs) based on previous approaches(Eichten, Stuart, Srivastava, Lister, & Borevitz, 2016).First, a strict approach was used to identify high confidence DMRs using Bayesian hierarchical modelling, at single cytosine resolution, using the R package DSS (v2.10.0;Feng, Conneely, & Wu, 2014)…”

mentioning

confidence: 99%

Maintenance of pre‐existing DNA methylation states through recurring excess‐light stress

Ganguly

Crisp

Eichten

et al. 2018

Plant Cell & Environment

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The capacity for plant stress priming and memory and the notion of this being underpinned by DNA methylation-mediated memory is an appealing hypothesis for which there is mixed evidence. We previously established a lack of drought-induced methylome variation in Arabidopsis thaliana (Arabidopsis); however, this was tied to only minor observations of physiological memory. There are numerous independent observations demonstrating that photoprotective mechanisms, induced by excess-light stress, can lead to robust programmable changes in newly developing leaf tissues. Although key signalling molecules and transcription factors are known to promote this priming signal, an untested question is the potential involvement of chromatin marks towards the maintenance of light stress acclimation, or memory. Thus, we systematically tested our previous hypothesis of a stress-resistant methylome using a recurring excess-light stress, then analysing new, emerging, and existing tissues. The DNA methylome showed negligible stress-associated variation, with the vast majority attributable to stochastic differences. Yet, photoacclimation was evident through enhanced photosystem II performance in exposed tissues, and nonphotochemical quenching and fluorescence decline ratio showed evidence of mitotic transmission. Thus, we have observed physiological acclimation in new and emerging tissues in the absence of substantive DNA methylome changes.

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“…B. distachyon reads for seven inbred lines [42] were also obtained from the SRA (Bd21, SRR1972494; Bd21-3, SRR1972495; Bd1-1, SRR1972498; Bd3-1, SRR1972496; Bd30-1, SRR1972497; BdTR12C, SRR1972499; Koz3, SRR1972500). Maize reads were mapped to the B73 reference genome version 2, and B. distachyon reads were mapped to the Bd21 v2 reference genome.…”

Section: Methodsmentioning

confidence: 99%

Proximal methylation features associated with nonrandom changes in gene body methylation

Picard

Gehring

2017

Genome Biol

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BackgroundGene body methylation at CG dinucleotides is a widely conserved feature of methylated genomes but remains poorly understood. The Arabidopsis thaliana strain Cvi has depleted gene body methylation relative to the reference strain Col. Here, we leverage this natural epigenetic difference to investigate gene body methylation stability.ResultsRecombinant inbred lines derived from Col and Cvi were used to examine the transmission of distinct gene body methylation states. The vast majority of genic CG methylation patterns are faithfully transmitted over nine generations according to parental genotype, with only 1–4% of CGs either losing or gaining methylation relative to the parent. Genic CGs that fail to maintain the parental methylation state are shared among independent lines, suggesting that these are not random occurrences. We use a logistic regression framework to identify features that best predict sites that fail to maintain parental methylation state. Intermediate levels of CG methylation around a dynamic CG site and high methylation variability across many A. thaliana strains at that site are the strongest predictors. These data suggest that the dynamic CGs we identify are not specific to the Col–Cvi recombinant inbred lines but have an epigenetic state that is inherently less stable within the A. thaliana species. Extending this, variably methylated genic CGs in maize and Brachypodium distachyon are also associated with intermediate local CG methylation.ConclusionsThese results provide new insights into the features determining the inheritance of gene body methylation and demonstrate that two different methylation equilibria can be maintained within single individuals.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1206-2) contains supplementary material, which is available to authorized users.

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DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

Cited by 37 publications

References 74 publications

The Aegilops tauschii genome reveals multiple impacts of transposons

The Aegilops tauschii genome reveals multiple impacts of transposons

Maintenance of pre‐existing DNA methylation states through recurring excess‐light stress

Proximal methylation features associated with nonrandom changes in gene body methylation

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