Blog
About

  • Record: found
  • Abstract: found
  • Article: found
Is Open Access

Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity

Read this article at

Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Abstract

      Inducible epigenetic changes in eukaryotes are believed to enable rapid adaptation to environmental fluctuations. We have found distinct regions of the Arabidopsis genome that are susceptible to DNA (de)methylation in response to hyperosmotic stress. The stress-induced epigenetic changes are associated with conditionally heritable adaptive phenotypic stress responses. However, these stress responses are primarily transmitted to the next generation through the female lineage due to widespread DNA glycosylase activity in the male germline, and extensively reset in the absence of stress. Using the CNI1/ATL31 locus as an example, we demonstrate that epigenetically targeted sequences function as distantly-acting control elements of antisense long non-coding RNAs, which in turn regulate targeted gene expression in response to stress. Collectively, our findings reveal that plants use a highly dynamic maternal ‘short-term stress memory’ with which to respond to adverse external conditions. This transient memory relies on the DNA methylation machinery and associated transcriptional changes to extend the phenotypic plasticity accessible to the immediate offspring.DOI: http://dx.doi.org/10.7554/eLife.13546.001

      eLife digest

      Most plants spend their entire lives in one fixed spot and so must be able to quickly adapt to any changes in their surroundings. For example, high levels of salt in the soil – which can be toxic to cells – triggers stress responses in plants that help them to mitigate any damage. Once the stress has passed, plants are able to retain a memory of it, which allows them to respond more quickly if they face the same stress in future. Furthermore, plants may pass on this ‘stress memory’ to their offspring.It is thought that stress memory is programmed by chemical modifications to DNA known as epigenetic marks. These marks do not alter the genetic information that is encoded by the DNA itself, but they can change the activity of particular genes. Environmental stress leads to changes in the epigenetic marks found on many plant genes, which can be directly passed on from the parent plant to its offspring. However, it was not clear whether the epigenetic marks that programme stress memory can be passed on in this way.Wibowo, Becker et al. investigated how a model plant called Arabidopsis thaliana is able to remember periods of salt stress. The experiments show that high levels of salt can trigger changes in the patterns of epigenetic marks associated with particular regions of DNA. This memory is reinforced by repetitive exposure to similar salt stress and can be passed onto offspring, primarily through the maternal line. However, this stress memory is not fixed in future generations as the epigenetic marks can be reset to their original patterns if plants find themselves growing and reproducing under non-stress conditions.In sum, the findings of Wibowo, Becker et al. show that epigenetic marks allow plants to inherit stress memory on a temporary basis while the stress is present, but to gradually lose the memory if the stress does not return. Future studies will focus on finding out if stress memory in crop plants works in the same way.DOI: http://dx.doi.org/10.7554/eLife.13546.002

      Related collections

      Most cited references 103

      • Record: found
      • Abstract: found
      • Article: not found

      Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

       K Livak,  T Schmittgen (2001)
      The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
        Bookmark
        • Record: found
        • Abstract: found
        • Article: found
        Is Open Access

        BEDTools: a flexible suite of utilities for comparing genomic features

        Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools Contact: aaronquinlan@gmail.com; imh4y@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
          Bookmark
          • Record: found
          • Abstract: found
          • Article: not found

          Circos: an information aesthetic for comparative genomics.

          We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.
            Bookmark

            Author and article information

            Affiliations
            [1 ]deptSchool of Life Sciences , University of Warwick , Coventry, United Kingdom
            [2 ]deptDepartment of Molecular Biology , Max Planck Institute for Developmental Biology , Tübingen, Germany
            [3 ]deptDepartment of Agricultural, Food and Environmental Science , University of Perugia , Perugia, Italy
            [4 ]Instituto Gulbenkian de Ciencia , Oeiras, Portugal
            University of California-Berkeley & USDA Agricultural Research Service , United States
            University of California-Berkeley & USDA Agricultural Research Service , United States
            Author notes
            [†]

            These authors contributed equally to this work.

            Contributors
            Role: Reviewing editor,
            University of California-Berkeley & USDA Agricultural Research Service , United States
            Journal
            eLife
            Elife
            eLife
            eLife
            eLife
            eLife Sciences Publications, Ltd
            2050-084X
            31 May 2016
            2016
            : 5
            27242129
            4887212
            13546
            10.7554/eLife.13546
            (Reviewing editor)
            © 2016, Wibowo et al

            This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

            Product
            Funding
            Funded by: FundRef http://dx.doi.org/10.13039/501100004189, Max-Planck-Gesellschaft;
            Award Recipient :
            Funded by: FundRef http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft;
            Award ID: SFB 1101- Project C01
            Award Recipient :
            Funded by: ESF/RTD Framework COST action;
            Award ID: FA0903
            Award Recipient :
            Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
            Award ID: BB/F008082
            Award Recipient :
            Funded by: EU FP7 Collaborative Project Grant;
            Award ID: AENEAS
            Award Recipient :
            Funded by: ERA-CAPS Project;
            Award ID: EVOREPRO
            Award Recipient :
            Funded by: The Royal Society;
            Award ID: IE150496
            Award Recipient :
            The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
            Categories
            Research Article
            Computational and Systems Biology
            Genomics and Evolutionary Biology
            Custom metadata
            2.5
            Transient adaptation to environmental fluctuations in plants is mediated through discrete epigenetic changes.

            Life sciences

            memory, environment, epigenetic, adaptation, <i>a. thaliana</i>

            Comments

            Comment on this article