The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
- Michael Regulski1,5,
- Zhenyuan Lu1,5,
- Jude Kendall1,5,
- Mark T.A. Donoghue1,
- Jon Reinders2,
- Victor Llaca2,
- Stephane Deschamps2,
- Andrew Smith3,
- Dan Levy1,
- W. Richard McCombie1,
- Scott Tingey2,
- Antoni Rafalski2,
- James Hicks1,
- Doreen Ware1,4 and
- Robert A. Martienssen1,6
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
- 2DuPont Crop Genetics Research, Experimental Station, Wilmington, Delaware 19880, USA;
- 3Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA;
- 4USDA-ARS NAA, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
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↵5 These authors contributed equally to this work.
Abstract
The maize genome, with its large complement of transposons and repeats, is a paradigm for the study of epigenetic mechanisms such as paramutation and imprinting. Here, we present the genome-wide map of cytosine methylation for two maize inbred lines, B73 and Mo17. CG (65%) and CHG (50%) methylation (where H = A, C, or T) is highest in transposons, while CHH (5%) methylation is likely guided by 24-nt, but not 21-nt, small interfering RNAs (siRNAs). Correlations with methylation patterns suggest that CG methylation in exons (8%) may deter insertion of Mutator transposon insertion, while CHG methylation at splice acceptor sites may inhibit RNA splicing. Using the methylation map as a guide, we used low-coverage sequencing to show that parental methylation differences are inherited by recombinant inbred lines. However, frequent methylation switches, guided by siRNA, persist for up to eight generations, suggesting that epigenetic inheritance resembling paramutation is much more common than previously supposed. The methylation map will provide an invaluable resource for epigenetic studies in maize.
Footnotes
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↵6 Corresponding author
E-mail martiens{at}cshl.edu
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.153510.112.
Freely available online through the Genome Research Open Access option.
- Received December 11, 2012.
- Accepted May 30, 2013.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.
