The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

• Published in: Genome research Vol. 23; no. 10; pp. 1651 - 1662
• Main Authors: Regulski, Michael, Lu, Zhenyuan, Kendall, Jude, Donoghue, Mark T A, Reinders, Jon, Llaca, Victor, Deschamps, Stephane, Smith, Andrew, Levy, Dan, McCombie, W Richard, Tingey, Scott, Rafalski, Antoni, Hicks, James, Ware, Doreen, Martienssen, Robert A
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.10.2013
• Subjects: Alternative Splicing; Cytosine; DNA Methylation; DNA Transposable Elements; DNA, Plant - genetics; DNA, Plant - metabolism; Epigenesis, Genetic; Exons; Gene Expression Regulation, Plant; Genome, Plant; Genomic Imprinting; RNA Splice Sites; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Plant - genetics; RNA, Plant - metabolism; RNA, Small Interfering - genetics; RNA, Small Interfering - metabolism; Sequence Analysis; Zea mays; Zea mays - genetics; Zea mays - metabolism
• ISSN: 1088-9051; 1549-5469
• DOI: 10.1101/gr.153510.112

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.