Biology subjects

Van Antro, M.

Publications and source records attributed to Van Antro, M..

3 recordsLinked to original sources

bioRxiv2023

DNA methylation responses to stress across different plant species

O_LIChanges in environments trigger plant DNA methylation responses, potentially modulating stress responses. Studies on stress-induced DNA methylation typically focus on single species, limiting our understanding of what are general and specific responses between species. C_LIO_LIUsing reduced-representation bisulfite sequencing epiGBS, we compared DNA methylation stress-responses across seven plant species. Because methylation can be targeted at transposable elements (TEs) and because environmental plasticity may be particularly relevant in asexual species, we hypothesize that genome size and reproduction mode explain differences in methylation responses between species. C_LIO_LIWe show that enrichment of environmentally-induced methylation responses in genes and TEs is a general feature across plant species. While previous studies have emphasized methylation responses in CHH-cytosines, we observed that cytosines in all sequence contexts (CG, CHG, CHH) are equally likely to respond to stress. Larger-genome species showed a higher proportion of stress-responding cytosines, and asexual species showed more cytosines with a strong methylation response to stress than sexually responding species. C_LIO_LIOur study highlights the role of TEs in methylome plasticity and identifies causes of variation in methylome plasticity. This provides guidance to extrapolating results from models to other plant species, and may contribute to better understanding of functionality of the response. C_LI

plant biology↗

bioRxiv2022

DNA methylation in clonal Duckweed lineages (Lemna minor L.) reflects current and historical environmental exposures.

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 reproduction of the common duckweed Lemna minor, we tested the hypothesis that a long-term, transgenerational stress memory from exposure to high temperature can be detected in DNA methylation profiles. Using a reduced representation bisulfite sequencing approach (epiGBS), we show that high temperature stress induces DNA hypermethylation at many cytosines in CG and CHG contexts but not in CHH. In addition, a subset of the temperature responsive CHG cytosines, showed differential DNA methylation between in lineages exposed to 30{degrees}C and 24{degrees}C, 3-12 clonal generations after subsequent culturing in a common environment, demonstrating a memory effect of stress that persists over many clonal generations and that is reflected in DNA methylation. Structural annotation revealed that this memory effect in CHG methylation was enriched in TEs. We argue that the observed epigenetic stress memory is likely caused by stable transgenerational persistence of high temperature-induced DNA methylation variants across multiple 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 and vegetatively propagated crops.

evolutionary biology↗

bioRxiv2020

epiGBS2: an improved protocol and automated snakemake workflow for highly multiplexed reduced representation bisulfite sequencing

epiGBS is an existing reduced representation bisulfite sequencing method to determine cytosine methylation and genetic polymorphisms de novo. Here, we present epiGBS2, an improved epiGBS laboratory protocol and user-friendly bioinformatics pipeline for a wide range of species with or without reference genome. epiGBS2 decreases costs and time investment and increases user-friendliness and reproducibility. The library protocol was adjusted to allow for a flexible choice of restriction enzymes and a double digest. Instead of fully methylated adapters, semi-methylated adapters are now used. The bioinformatics pipeline was improved in speed and integrated in the snakemake workflow management system, which now makes the pipeline easy to execute, modular, and parameter settings flexible. We also provide a detailed description of the laboratory protocol, an extensive manual of the bioinformatics pipeline, which is publicly accessible on github (https://github.com/nioo-knaw/epiGBS2) and zenodo (https://doi.org/10.5281/zenodo.3819996), and example output.

bioinformatics↗