Статья

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

Michael RegulskiCold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;Zhenyuan Lu1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;Jude Kendall1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;Mark T.A. Donoghue1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;Jon Reinders2DuPont Crop Genetics Research, Experimental Station, Wilmington, Delaware 19880, USA;Víctor Llaca2DuPont Crop Genetics Research, Experimental Station, Wilmington, Delaware 19880, USA;Stéphane Deschamps2DuPont Crop Genetics Research, Experimental Station, Wilmington, Delaware 19880, USA;Andrew D. Smith3Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA;Dan Levy1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;W. Richard McCombie1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;Scott Tingey2DuPont Crop Genetics Research, Experimental Station, Wilmington, Delaware 19880, USA;Antoni Rafalski2DuPont Crop Genetics Research, Experimental Station, Wilmington, Delaware 19880, USA;James Hicks1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;Doreen Ware1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;Robert A. Martienssen1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;

2013en

ABI

Аннотация

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.

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Идентификаторы

DOI: 10.1101/gr.153510.112

Цитирования и источники

Цитирований: 2Использованных источников: 0

Показатели — AkademScholar