title: The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA.
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.
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
authors.forename: Michael
authors.initials: M
authors.lastname: Regulski
authors.forename: Zhenyuan
authors.initials: Z
authors.lastname: Lu
authors.forename: Jude
authors.initials: J
authors.lastname: Kendall
authors.forename: Mark T A
authors.initials: MT
authors.lastname: Donoghue
authors.forename: Jon
authors.initials: J
authors.lastname: Reinders
authors.forename: Victor
authors.initials: V
authors.lastname: Llaca
authors.forename: Stephane
authors.initials: S
authors.lastname: Deschamps
authors.forename: Andrew
authors.initials: A
authors.lastname: Smith
authors.forename: Dan
authors.initials: D
authors.lastname: Levy
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Scott
authors.initials: S
authors.lastname: Tingey
authors.forename: Antoni
authors.initials: A
authors.lastname: Rafalski
authors.forename: James
authors.initials: J
authors.lastname: Hicks
authors.forename: Doreen
authors.initials: D
authors.lastname: Ware
authors.forename: Robert A
authors.initials: RA
authors.lastname: Martienssen
mesh_terms: D017398:Alternative Splicing; D019175:DNA Methylation; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics* / Q000378:metabolism; D044127:Epigenesis, Genetic; D005091:Exons; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D018392:Genomic Imprinting; D022821:RNA Splice Sites; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism; D017421:Sequence Analysis; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism*
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant; D022821:RNA Splice Sites; D012333:RNA, Messenger; D018749:RNA, Plant; D034741:RNA, Small Interfering