Journal
PLANT JOURNAL
Volume 63, Issue 3, Pages 353-365Publisher
WILEY-BLACKWELL
DOI: 10.1111/j.1365-313X.2010.04246.x
Keywords
cytosine methylation; Illumina sequencing; centromere; epigenomics; rice
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Funding
- National Science Foundation [DBI-0603927, DBI-0923640]
- US Department of Energy's Office of Science
- University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]
- Lawrence Livermore National Laboratory [DE-AC52-07NA27344]
- Los Alamos National Laboratory [DE-AC02-06NA25396]
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [0923640] Funding Source: National Science Foundation
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P>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.
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