Similarity between soybean and
            <i>Arabidopsis</i>
            seed methylomes and loss of non-CG methylation does not affect seed development

Lin, Jer-Young; Le, Brandon H.; Chen, Min; Henry, Kelli F.; Hur, Jungim; Hsieh, Tzung‐Fu; Chen, Pao‐Yang; Pelletier, Julie; Pellegrini, Matteo; Fischer, Robert L.; Harada, John J.; Goldberg, Robert B.

doi:10.1073/pnas.1716758114

Cited by 120 publications

(195 citation statements)

References 62 publications

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“…In wheat allotetraploids, the dramatic changes in small RNAs and chromatin modifications such as H3K9me2 in AADD could alter the expression of TEs and the formation of aneuploids in AADD (Zhang et al ., ), which is also a factor behind genome instability. Activation of TE is commonly observed during seed development in Arabidopsis (Gehring et al ., ; Hsieh et al ., ), soybean (Lin et al ., ) and rice (Luo et al ., ; Yuan et al ., ). Activation of TEs in vegetative tissues is rare; however, a recent study found that activation of TEs in rice roots could act as a decoy for microRNA regulation (Cho and Paszkowski, ).…”

Section: Discussionmentioning

confidence: 99%

Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids

Yuan

Jiang

et al. 2018

The Plant Journal

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Polyploidy occurs in some animals and all flowering plants, including important crops such as wheat. The consequences of polyploidy in crops remain elusive, partly because their progenitors are unknown. Using two resynthesized wheat allotetraploids S S AA and AADD with known diploid progenitors, we analyzed mRNA and small RNA transcriptomes in the endosperm, compared transcriptomes between endosperm and root in AADD, and examined chromatin changes in the allotetraploids. In the endosperm, there were more non-additively expressed genes in S S AA than in AADD. In AADD, non-additively expressed genes were developmentally regulated, and the majority (62-70%) were repressed. The repressed genes in AADD included a group of histone methyltransferase gene homologs, which correlated with reduced histone H3K9me2 levels and activation of various transposable elements in AADD. In S S AA, there was a tendency for expression dominance of S over A homoeologs, but the histone methyltransferase gene homologs were additively expressed, correlating with insignificant changes in histone H3K9me2 levels. Moreover, more 24-nucleotide small inferring RNAs (siRNAs) in the A subgenome were disrupted in AADD than in S S AA, which were associated with expression changes of siRNA-associated genes. Our results indicate that asymmetrical changes in siRNAs, chromatin modifications, transposons and gene expression coincide with unstable AADD genomes and stable S S AA genomes, which could help explain the evolutionary trajectories of wheat allotetraploids formed by different progenitors.

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Section: Discussionmentioning

confidence: 99%

Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids

Yuan

Jiang

et al. 2018

The Plant Journal

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“…Wild-type sperm has low CHH methylation (Calarco et al, 2012), indicating that the paternal genome must gain methylation after fertilization. Recent studies from soybean and Arabidopsis have shown that CHH methylation increases during embryogenesis (Kawakatsu et al, 2017;Lin et al, 2017;Narsai et al, 2017). In mature Arabidopsis embryos, CHH methylation approaches 100% at individual cytosines, whereas in other tissues, including younger embryos, individual CHH sites are c. 20% methylated (Bouyer et al, 2017).…”

Section: Heritability and Reinforcement Of Dna Methylation In Thementioning

confidence: 99%

“…In mature Arabidopsis embryos, CHH methylation approaches 100% at individual cytosines, whereas in other tissues, including younger embryos, individual CHH sites are c. 20% methylated (Bouyer et al, 2017). Methylation decreases upon seed germination, likely through a passive mechanism (Bouyer et al, 2017;Kawakatsu et al, 2017;Lin et al, 2017;Narsai et al, 2017). It is unknown whether the increased CHH methylation in developing embryos is functional: mutation of the de novo methyltransferases DRM2 and CMT2 prevents CHH methylation but without obvious effects on seed development or germination, although it is unclear how comprehensively phenotypes have been assessed.…”

Section: Heritability and Reinforcement Of Dna Methylation In Thementioning

confidence: 99%

Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?

Gehring

2019

New Phytologist

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Summary Over the last 10 yr there have been major advances in documenting and understanding dynamic changes to DNA methylation, small RNAs, chromatin modifications and chromatin structure that accompany reproductive development in flowering plants, from germline specification to seed maturation. Here I highlight recent advances in the field, mostly made possible by microscopic analysis of epigenetic states or by the ability to isolate specific cell types or tissues and apply omics approaches. I consider in which contexts there is potentially reprogramming vs maintenance or reinforcement of epigenetic states.

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“…The protocol outlined above was also applied to A. thaliana and rice. Classification of CpGs (but also CHG and CHH sites) into methylated and unmethylated sites was based on bisulfite data of Ws0 global stage seed for A. thaliana (GSM1664380) (Lin et al 2017) , and data from 3-week old leaf tissue in rice (GSM1039487) (Stroud et al 2013). As highlighted above, to calculate rare SNP incidence, we considered homozygous SNPs confined to a single accession in the selfing A. thaliana as singletons.…”

Section: Analysis Of Relative Mutational Risk Associated With Methylamentioning

confidence: 99%

Cytosine methylation affects the mutability of neighbouring nucleotides in human, Arabidopsis, and rice

Kusmartsev

Warnecke

2019

Preprint

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Methylated cytosines deaminate at higher rates than unmethylated cytosines and the lesions they produce are repaired less efficiently. As a result, methylated cytosines are mutational hotspots. Here, combining rare polymorphism and base-resolution methylation data in humans, Arabidopsis thaliana, and rice (Oryza sativa), we present evidence that methylation state affects mutation dynamics not only at the focal cytosine but also at neighbouring nucleotides. In humans, contrary to prior suggestions, we find that nucleotides in the close vicinity (±3nt) of methylated cytosines mutate less frequently. In contrast, methylation is associated with increased neighbourhood mutation risk in A. thaliana and rice. The difference in mutation risk associated with methylation is less pronounced further away from the focal CpG, is modulated by regional GC content, and enhanced in heterochromatic regions. Our results are consistent with a model where elevated risk at neighbouring bases is linked to lesion formation at the focal cytosine and subsequent long-patch repair. Our results provide evidence that cytosine methylation has a broader mutational footprints than commonly assumed. They also illustrate that methylation is not intrinsically associated with higher mutation risk for surrounding bases, but that mutagenic effects reflect evolved speciesspecific and lesion-specific predispositions to elicit error-prone long-patch DNA repair.

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Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development

Cited by 120 publications

References 62 publications

Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids

Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids

Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?

Cytosine methylation affects the mutability of neighbouring nucleotides in human, Arabidopsis, and rice

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