1. Genetics and Genomics
  2. Plant Biology

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

  1. Daniela Pignatta
  2. Robert M Erdmann
  3. Elias Scheer
  4. Colette L Picard
  5. George W Bell
  6. Mary Gehring  Is a corresponding author
  1. Whitehead Institute for Biomedical Research, United States
https://doi.org/10.7554/eLife.03198
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  1. Daniela Pignatta
  2. Robert M Erdmann
  3. Elias Scheer
  4. Colette L Picard
  5. George W Bell
  6. Mary Gehring
(2014)
Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting
eLife 3:e03198.
https://doi.org/10.7554/eLife.03198
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Abstract

Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.

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Author details

  1. Daniela Pignatta

    Whitehead Institute for Biomedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Robert M Erdmann

    Whitehead Institute for Biomedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Elias Scheer

    Whitehead Institute for Biomedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Colette L Picard

    Whitehead Institute for Biomedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. George W Bell

    Whitehead Institute for Biomedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Mary Gehring

    Whitehead Institute for Biomedical Research, Cambridge, United States
    For correspondence
    mgehring@wi.mit.edu
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Detlef Weigel, Max Planck Institute for Developmental Biology, Germany

Version history

  1. Received: April 25, 2014
  2. Accepted: July 2, 2014
  3. Accepted Manuscript published: July 3, 2014 (version 1)
  4. Version of Record published: August 5, 2014 (version 2)
  5. Version of Record updated: April 7, 2017 (version 3)
  6. Version of Record updated: June 6, 2017 (version 4)

Copyright

© 2014, Pignatta et al.

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

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  1. Daniela Pignatta
  2. Robert M Erdmann
  3. Elias Scheer
  4. Colette L Picard
  5. George W Bell
  6. Mary Gehring
(2014)
Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting
eLife 3:e03198.
https://doi.org/10.7554/eLife.03198

Share this article

https://doi.org/10.7554/eLife.03198

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