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      DNA methylation changes induced by long and short photoperiods in Nasonia

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          Abstract

          Many organisms monitor the annual change in day length and use this information for the timing of their seasonal response. However, the molecular mechanisms underlying photoperiodic timing are largely unknown. The wasp Nasonia vitripennis is an emerging model organism that exhibits a strong photoperiodic response: Short autumnal days experienced by females lead to the induction of developmental arrest (diapause) in their progeny, allowing winter survival of the larvae. How female Nasonia control the developmental trajectory of their offspring is unclear. Here, we took advantage of the recent discovery that DNA methylation is pervasive in Nasonia and tested its role in photoperiodism. We used reduced representation bisulfite sequencing (RRBS) to profile DNA methylation in adult female wasps subjected to different photoperiods and identified substantial differential methylation at the single base level. We also show that knocking down DNA methyltransferase 1a (Dnmt1a), Dnmt3, or blocking DNA methylation pharmacologically, largely disrupts the photoperiodic diapause response of the wasps. To our knowledge, this is the first example for a role of DNA methylation in insect photoperiodic timing.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            The Sequence Alignment/Map format and SAMtools

            Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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              Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

              Summary: A combination of bisulfite treatment of DNA and high-throughput sequencing (BS-Seq) can capture a snapshot of a cell's epigenomic state by revealing its genome-wide cytosine methylation at single base resolution. Bismark is a flexible tool for the time-efficient analysis of BS-Seq data which performs both read mapping and methylation calling in a single convenient step. Its output discriminates between cytosines in CpG, CHG and CHH context and enables bench scientists to visualize and interpret their methylation data soon after the sequencing run is completed. Availability and implementation: Bismark is released under the GNU GPLv3+ licence. The source code is freely available from www.bioinformatics.bbsrc.ac.uk/projects/bismark/. Contact: felix.krueger@bbsrc.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Journal
                Genome Res
                Genome Res
                genome
                genome
                GENOME
                Genome Research
                Cold Spring Harbor Laboratory Press
                1088-9051
                1549-5469
                February 2016
                February 2016
                : 26
                : 2
                : 203-210
                Affiliations
                [1 ]Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom;
                [2 ]School of Biology, University of St Andrews, St Andrews KY16 9TH, United Kingdom
                Author notes
                [3]

                These authors contributed equally to this work.

                Corresponding author: et22@ 123456le.ac.uk
                Article
                9509184
                10.1101/gr.196204.115
                4728373
                26672019
                3825e4a9-3ca0-4c69-9b6d-8ff49a70009c
                © 2016 Pegoraro et al.; Published by Cold Spring Harbor Laboratory Press

                This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

                History
                : 22 June 2015
                : 14 December 2015
                Page count
                Pages: 8
                Funding
                Funded by: Biotechnology and Biological Sciences Research Council http://dx.doi.org/10.13039/501100000268
                Award ID: BB/K001922/1
                Award ID: BB/J014532/1
                Funded by: Natural Environment Research Council http://dx.doi.org/10.13039/501100000270
                Award ID: NE/J024481/1
                Categories
                Research

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