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      EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels

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          Abstract

          The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a program that detects both new transposable element insertion sites and their methylation states from a single MethylC-seq dataset. EpiTEome outperforms other split-read insertion site detection programs, even while functioning on bisulfite-converted reads. EpiTEome characterizes the previously discarded fraction of DNA methylation at sites of new insertions, enabling future investigation into the epigenetic regulation of non-reference and transposed elements.

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          Whole-genome sequencing of multiple Arabidopsis thaliana populations.

          Jun Cao, Korbinian Schneeberger, Stephan Ossowski … (2011)
          The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations.
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            eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses

            Luana Micallef, Peter Rodgers (2014)
            Venn diagrams with three curves are used extensively in various medical and scientific disciplines to visualize relationships between data sets and facilitate data analysis. The area of the regions formed by the overlapping curves is often directly proportional to the cardinality of the depicted set relation or any other related quantitative data. Drawing these diagrams manually is difficult and current automatic drawing methods do not always produce appropriate diagrams. Most methods depict the data sets as circles, as they perceptually pop out as complete distinct objects due to their smoothness and regularity. However, circles cannot draw accurate diagrams for most 3-set data and so the generated diagrams often have misleading region areas. Other methods use polygons to draw accurate diagrams. However, polygons are non-smooth and non-symmetric, so the curves are not easily distinguishable and the diagrams are difficult to comprehend. Ellipses are more flexible than circles and are similarly smooth, but none of the current automatic drawing methods use ellipses. We present eulerAPE as the first method and software that uses ellipses for automatically drawing accurate area-proportional Venn diagrams for 3-set data. We describe the drawing method adopted by eulerAPE and we discuss our evaluation of the effectiveness of eulerAPE and ellipses for drawing random 3-set data. We compare eulerAPE and various other methods that are currently available and we discuss differences between their generated diagrams in terms of accuracy and ease of understanding for real world data.
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              Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis.

              Tomoko Toyama, Keitaro Watanabe, S Yonebayashi … (2001)
              A major component of the large genomes of higher plants and vertebrates comprises transposable elements and their derivatives, which potentially reduce the stability of the genome. It has been proposed that methylation of cytosine residues may suppress transposition, but experimental evidence for this has been limited. Reduced methylation of repeat sequences results from mutations in the Arabidopsis gene DDM1 (decrease in DNA methylation), which encodes a protein similar to the chromatin-remodelling factor SWI2/SNF2 (ref. 7). In the ddm1-induced hypomethylation background, silent repeat sequences are often reactivated transcriptionally, but no transposition of endogenous elements has been observed. A striking feature of the ddm1 mutation is that it induces developmental abnormalities by causing heritable changes in other loci. Here we report that one of the ddm1-induced abnormalities is caused by insertion of CAC1, an endogenous CACTA family transposon. This class of Arabidopsis elements transposes and increases in copy number at high frequencies specifically in the ddm1 hypomethylation background. Thus the DDM1 gene not only epigenetically ensures proper gene expression, but also stabilizes transposon behaviour, possibly through chromatin remodelling or DNA methylation.
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                Author and article information

                Contributors
                Josquin Daron: daron.6@osu.edu
                R. Keith Slotkin:
                ORCID: http://orcid.org/0000-0001-9582-3533
                Slotkin.2@osu.edu
                Journal
                Journal ID (nlm-ta): Genome Biol
                Journal ID (iso-abbrev): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central (London )
                ISSN (Print): 1474-7596
                ISSN (Electronic): 1474-760X
                Publication date (Electronic): 12 May 2017
                Publication date PMC-release: 12 May 2017
                Publication date Collection: 2017
                Volume: 18
                Electronic Location Identifier: 91
                Affiliations
                ISNI 0000 0001 2285 7943, GRID grid.261331.4, Department of Molecular Genetics, , The Ohio State University, ; Columbus, OH USA
                Author information
                http://orcid.org/0000-0001-9582-3533
                Article
                Publisher ID: 1232
                DOI: 10.1186/s13059-017-1232-0
                PMC ID: 5429532
                PubMed ID: 28499400
                SO-VID: 09b8d199-c9f0-4ac4-857b-3e81f668237a
                Copyright © © The Author(s). 2017
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 31 January 2017
                Date accepted : 5 May 2017
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000076, Directorate for Biological Sciences;
                Award ID: MCB-1252370
                Award Recipient :
                Categories
                Subject: Software
                Custom metadata
                issue-copyright-statement © The Author(s) 2017

                ScienceOpen disciplines: Genetics
                Keywords: methylome,transposable elements,insertion site,bisulfite,split reads,bioinformatics,methylc-seq
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: methylome, transposable elements, insertion site, bisulfite, split reads, bioinformatics, methylc-seq

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