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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #295001
Title: The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

Author
item REGULSKI, MICHAEL - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item KENDALL, JUDE - Cold Spring Harbor Laboratory
item DONOGHUE, MARK - Cold Spring Harbor Laboratory
item REINDERS, JON - Dupont Crop Genetics
item LLACA, VICTOR - Dupont Crop Genetics
item DESCHAMPS, STEPHANE - Dupont Crop Genetics
item SMITH, ANDREW - University Of Southern California
item LEVY, DAN - Cold Spring Harbor Laboratory
item MCCOMBIE, RICHARD - Cold Spring Harbor Laboratory
item TINGEY, SCOTT - Dupont Crop Genetics
item RAFALSKI, ANTONI - Dupont Crop Genetics
item HICKS, JAMES - Cold Spring Harbor Laboratory
item Ware, Doreen
item MARTIENSSEN, ROBERT - Cold Spring Harbor Laboratory

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/31/2013
Publication Date: 6/5/2013
Citation: Regulski, M., Lu, Z., Kendall, J., Donoghue, M.T., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., Mccombie, R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., Martienssen, R.A. 2013. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research. DOI: 10.1101/gr.153510.112.

Interpretive Summary: DNA methylation is a critical epigenetic regulator in plant development. It is shown that methylation is associated with DNA replication, histone modification, and RNA interference. Some of the variation for many traits not explained by sequence variation might be due to DNA methylation. This article presents the genome-wide map of cytosine methylation for two maize inbred lines, B73 and Mo17, in single nucleotide resolution. Using this resource, we identified thousands of differentially methylated regions throughout maize genome and the differential methylation between inbred lines is largely heritable, and correlated with expression of nearby genes. Future studies using low coverage methylome sequencing can take advantage of this resource to determine the impact of differentially methylated regions on gene expression, chromosome biology, and transgenerational inheritance. For example, this will allow breeders to determine the contribution of cytosine methylation to phenotypic variation among elite inbreds and hybrids, artificially induced chromosomal variants (such as doubled haploids), and clonally micropropagated strains, which are subject to such epigenetic variation.

Technical Abstract: Background Maize exhibits a wealth of epigenetic phenomena, from transposon silencing, cycling and presetting, to gene imprinting and paramutation. Furthermore, despite the complexity and sophistication of maize breeding, there is a large degree of “hidden” variation for many traits that is difficult to explain by allelic variation alone. At least some of this unexplained variation might be due to epigenetic rather than genetic changes in the maize genome. Results We have used very-high-coverage whole genome bisulfite sequencing to explore DNA methylation at nucleotide resolution in genes, transposons, and other features of the maize genome, as well as its heritability and potential contribution to traits. We have found that methylation in different sequence contexts is guided differentially by small RNA, and is correlated with transposon insertion and mRNA splicing. Heritable and predictable switches in DNA methylation were detected in recombinant inbred lines. These shifts were apparently triggered by small RNA, resembling paramutation, but then maintained by replication-dependent symmetric methylation. Conclusions We have determined the nucleotide-resolution methylation map of the maize genome. Methylation of transposons and repeats is highly conserved between inbred lines, but methylation of gene bodies is much more variable and includes splice site and exon methylation in differing contexts. CHG acceptor splice site methylation is correlated with reduced splicing efficiency, while CG methylation of exons seems to deter disruption of highly expressed genes by transposon insertion. Differential methylation between inbred lines is largely heritable, and correlated with expression of nearby genes, but thousands of highly differentially methylated regions throughout the genome shift from one epi-allele to the other and are stably inherited in recombinant inbred lines.