TY  - JOUR
A1  - Regulski, Michael
A1  - Lu, Zhenyuan
A1  - Kendall, Jude
A1  - Donoghue, Mark T.A.
A1  - Reinders, Jon
A1  - Llaca, Victor
A1  - Deschamps, Stephane
A1  - Smith, Andrew
A1  - Levy, Dan
A1  - McCombie, W. Richard
A1  - Tingey, Scott
A1  - Rafalski, Antoni
A1  - Hicks, James
A1  - Ware, Doreen
A1  - Martienssen, Robert A.
T1  - The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
Y1  - 2013/10/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1651 
EP  - 1662 
DO  - 10.1101/gr.153510.112 
VL  - 23 
IS  - 10 
UR  - http://genome.cshlp.org/content/23/10/1651.abstract 
N2  - 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. 
ER  -