Abstract:While some DNA methylation variants are transgenerationally stable in plants, DNA methylation modifications that are specifically induced by environmental exposure are typically transient and subject to resetting in germ lines, limiting the potential for transgenerational epigenetics stress memory. Asexual reproduction circumvents germlines, and may be more conducive to long-term memory and inheritance of epigenetic marks. This, however, has been poorly explored. Taking advantage of the rapid clonal reproducti… Show more
“…PRJNA883550). The filtered methylation data, epiGBS de novo reference, as well as all phenotypic data we deposited in Zenodo (Van Antro et al, 2022a , 2022b ; DOI 10.5281/Zenodo.5680942 ). All analysis R scripts and the epiGBS pipeline scripts corresponding to the pipeline version used to obtain the methylation data have been made publicly accessible via gitlab: https://gitlab.bioinf.nioo.knaw.nl/MorganeA/script‐for‐l.minor‐paper.git .…”
Environmentally induced DNA methylation variants may mediate gene expression responses to environmental changes. If such induced variants are transgenerationally stable, there is potential for expression responses to persist over multiple generations. Our current knowledge in plants, however, is almost exclusively based on studies conducted in sexually reproducing species where the majority of DNA methylation changes are subject to resetting in germlines, limiting the potential for transgenerational epigenetics stress memory. Asexual reproduction circumvents germlines, and may therefore be more conducive to long-term inheritance of epigenetic marks. Taking advantage of the rapid clonal reproduction of the common duckweed Lemna minor, we hypothesize that long-term, transgenerational stress memory from exposure to high temperature can be detected in DNA methylation profiles. Using a reduced representation bisulphite sequencing approach (epiGBS), we show that temperature stress induces DNA hypermethylation at many CG and CHG cytosine contexts but not CHH. Additionally, differential methylation in CHG context that was observed was still detected in a subset of cytosines, even after 3-12 generations of culturing in a common environment. This demonstrates a memory effect of stress reflected in the methylome and that persists over multiple clonal generations. Structural annotation revealed that this memory effect in CHG methylation was enriched in transposable elements. The observed epigenetic stress memory is probably caused by stable transgenerational persistence of temperature-induced DNA methylation variants across clonal generations. To the extent that such epigenetic memory has functional consequences for gene expression and phenotypes, this result suggests potential for long-term modulation of stress responses in asexual plants.
“…PRJNA883550). The filtered methylation data, epiGBS de novo reference, as well as all phenotypic data we deposited in Zenodo (Van Antro et al, 2022a , 2022b ; DOI 10.5281/Zenodo.5680942 ). All analysis R scripts and the epiGBS pipeline scripts corresponding to the pipeline version used to obtain the methylation data have been made publicly accessible via gitlab: https://gitlab.bioinf.nioo.knaw.nl/MorganeA/script‐for‐l.minor‐paper.git .…”
Environmentally induced DNA methylation variants may mediate gene expression responses to environmental changes. If such induced variants are transgenerationally stable, there is potential for expression responses to persist over multiple generations. Our current knowledge in plants, however, is almost exclusively based on studies conducted in sexually reproducing species where the majority of DNA methylation changes are subject to resetting in germlines, limiting the potential for transgenerational epigenetics stress memory. Asexual reproduction circumvents germlines, and may therefore be more conducive to long-term inheritance of epigenetic marks. Taking advantage of the rapid clonal reproduction of the common duckweed Lemna minor, we hypothesize that long-term, transgenerational stress memory from exposure to high temperature can be detected in DNA methylation profiles. Using a reduced representation bisulphite sequencing approach (epiGBS), we show that temperature stress induces DNA hypermethylation at many CG and CHG cytosine contexts but not CHH. Additionally, differential methylation in CHG context that was observed was still detected in a subset of cytosines, even after 3-12 generations of culturing in a common environment. This demonstrates a memory effect of stress reflected in the methylome and that persists over multiple clonal generations. Structural annotation revealed that this memory effect in CHG methylation was enriched in transposable elements. The observed epigenetic stress memory is probably caused by stable transgenerational persistence of temperature-induced DNA methylation variants across clonal generations. To the extent that such epigenetic memory has functional consequences for gene expression and phenotypes, this result suggests potential for long-term modulation of stress responses in asexual plants.
“…Although not statistically significant after correcting for false discovery rate, patterns of differential methylation in the CHG context (and to a lesser extent in the CHH context) were much more localised than in the CpG context, suggesting this context may have a functional role in S. dumicola. Intriguingly, recent work in plants has suggested that differential methylation in non-CpG contexts may be associated with environmental variation and response to stress (Li et al, 2020;López et al, 2022;Antro et al, 2022). For example, woodland strawberry (Fragaria vesca) show global decrease of 1.8% in CHG methylation in response to salt stress and an increase of 3.1% when challenged with simulated hormone stress, while differential methylation was more common in the CHH context than either of the CpG or CHG contexts (López et al, 2022).…”
Living at high density and with low genetic diversity are factors that should both increase the susceptibility of organisms to disease. Therefore, group living organisms, especially those that are inbred, should be especially vulnerable to infection and therefore have particular strategies to cope with infection. Phenotypic plasticity, underpinned by epigenetic changes, could allow group living organisms to rapidly respond to infection challenges. To explore the potential role of epigenetic modifications in the immune response to a group-living species with low genetic diversity, we compared the genome-wide DNA methylation profiles of five colonies of social spiders (Stegodyphus dumicola) in their natural habitat in Namibia at the point just before they succumbed to infection to a point at least six months previously where they were presumably healthier. We found increases in genome- and chromosome-wide methylation levels in the CpG, CHG, and CHH contexts, although the genome-wide changes were not clearly different from zero. These changes were most prominent in the CHG context, especially at a narrow region of chromosome 13, hinting at an as-of-yet unsuspected role of this DNA methylation context in phenotypic plasticity. However, there were few clear patterns of differential methylation at the base level, and genes with a known immune function in spiders had mean methylation changes close to zero. Our results suggest that DNA methylation may change with infection at large genomic scales, but that this type of epigenetic change is not necessarily integral to the immune response of social spiders.
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