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Plant Epigenetics and Epigenomics pp 173–201Cite as

Identification and Comparison of Imprinted Genes Across Plant Species

Part of the Methods in Molecular Biology book series (MIMB,volume 2093)

Abstract

Genomic imprinting is a phenomenon that occurs in flowering plants and mammals, whereby a gene is expressed in a parent-of-origin-specific manner. Although imprinting has now been examined genome-wide in a number of species using RNA-seq, the analyses used to assess imprinting vary between studies, making consistent comparisons between species difficult. Here we present a simple, easy-to-use bioinformatic pipeline for imprinting analyses suitable for any tissue, including plant endosperm. All relevant scripts can be downloaded. As an illustrative example, we reanalyze published data from A. thaliana and Z. mays endosperm using the pipeline and then demonstrate how to use the results to assess the conservation of imprinting between these species. We also introduce the Plant Imprinting Database, a repository for published imprinting datasets in plants that can be used to view, compare, and download data.

Key words

  • Genomic imprinting
  • Plant Imprinting Database
  • Imprinting pipeline
  • Imprinting conservation

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Acknowledgments

We would like to thank Andy Nutter-Upham and Scott McCallum for their tireless work in building the imprinting database and Daniela Pignatta for initial contributions to database design.

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Authors and Affiliations

  1. Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA

    Colette L. Picard & Mary Gehring

  2. Whitehead Institute for Biomedical Research, Cambridge, MA, USA

    Colette L. Picard & Mary Gehring

  3. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA

    Mary Gehring

Authors
  1. Colette L. Picard
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  2. Mary Gehring
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Correspondence to Mary Gehring .

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Editors and Affiliations

  1. Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland

    Charles Spillane

  2. Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland

    Peter McKeown

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Picard, C.L., Gehring, M. (2020). Identification and Comparison of Imprinted Genes Across Plant Species. In: Spillane, C., McKeown, P. (eds) Plant Epigenetics and Epigenomics . Methods in Molecular Biology, vol 2093. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0179-2_13

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  • DOI: https://doi.org/10.1007/978-1-0716-0179-2_13

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