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

Regulski, M., Lu, Z., Kendall, J., Donoghue, M. T., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., McCombie, W. R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., Martienssen, R. (2013) The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research, 23 (10). pp. 1651-1662. ISSN 10889051 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/23739895
DOI: 10.1101/gr.153510.112

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 24nt, but not 21nt, small interfering RNA (siRNA). 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 8 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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
organism description > plant > maize
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mRNA dynamics
organism description > plant
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > sRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > splice site
CSHL Authors:
Communities: CSHL labs > Hicks lab
CSHL labs > Martienssen lab
CSHL labs > McCombie lab
CSHL labs > Ware lab
Depositing User: Matt Covey
Date Deposited: 24 Jun 2013 20:28
Last Modified: 18 Dec 2014 17:23
PMCID: PMC3787262
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28364

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