title: Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice.
abstract: We conducted genome-wide mapping of cytosine methylation using methylcytosine immunoprecipitation combined with Illumina sequencing. The chromosomal distribution pattern of methylated DNA is similar to the heterochromatin distribution pattern on rice chromosomes. The DNA methylation patterns of rice genes are similar to those in Arabidopsis thaliana, including distinct methylation patterns asssociated with gene bodies and promoters. The DNA sequences in the core domains of rice Cen4, Cen5 and Cen8 showed elevated methylation levels compared with sequences in the pericentromeric regions. In addition, elevated methylation levels were associated with the DNA sequences in the CENH3-binding subdomains, compared with the sequences in the flanking H3 subdomains. In contrast, the centromeric domain of Cen11, which is composed exclusively of centromeric satellite DNA, is hypomethylated compared with the pericentromeric domains. Thus, the DNA sequences associated with functional centromeres can be either hypomethylated or hypermethylated. The methylation patterns of centromeric DNA appear to be correlated with the composition of the associated DNA sequences. We propose that both hypomethylation and hypermethylation of CENH3-associated DNA sequences can serve as epigenetic marks to distinguish where CENH3 deposition will occur within the surrounding H3 chromatin.
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USAU.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Huihuang
authors.initials: H
authors.lastname: Yan
authors.forename: Shinji
authors.initials: S
authors.lastname: Kikuchi
authors.forename: Pavel
authors.initials: P
authors.lastname: Neumann
authors.forename: Wenli
authors.initials: W
authors.lastname: Zhang
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Wu
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
authors.forename: Jiming
authors.initials: J
authors.lastname: Jiang
mesh_terms: D002503:Centromere; D003596:Cytosine / Q000378:metabolism*; D019175:DNA Methylation; D017343:Genes, Plant; D012275:Oryza / Q000235:genetics*; D011401:Promoter Regions, Genetic; D011995:Recombination, Genetic
chemical_list: D003596:Cytosine