Genomic distribution of H3K9me2 and DNA methylation in a maize genome

Patrick T West; Qing Li; Lexiang Ji; Steven R Eichten; Jawon Song; Matthew W Vaughn; Robert J Schmitz; Nathan M Springer

doi:10.1371/journal.pone.0105267

Genomic distribution of H3K9me2 and DNA methylation in a maize genome

PLoS One. 2014 Aug 14;9(8):e105267. doi: 10.1371/journal.pone.0105267. eCollection 2014.

Authors

Patrick T West¹, Qing Li¹, Lexiang Ji², Steven R Eichten¹, Jawon Song³, Matthew W Vaughn³, Robert J Schmitz⁴, Nathan M Springer¹

Affiliations

¹ Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America.
² Department of Genetics, University of Georgia, Athens, Georgia, United States of America; Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America.
³ Texas Advanced Computing Center, University of Texas-Austin, Austin, Texas, United States of America.
⁴ Department of Genetics, University of Georgia, Athens, Georgia, United States of America.

Abstract

DNA methylation and dimethylation of lysine 9 of histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a complex landscape of interspersed genes and transposons. The genome-wide distribution of DNA methylation and H3K9me2 were investigated in seedling tissue for the maize inbred B73 and compared to patterns of these modifications observed in Arabidopsis thaliana. Most maize transposons are highly enriched for DNA methylation in CG and CHG contexts and for H3K9me2. In contrast to findings in Arabidopsis, maize CHH levels in transposons are generally low but some sub-families of transposons are enriched for CHH methylation and these families exhibit low levels of H3K9me2. The profile of modifications over genes reveals that DNA methylation and H3K9me2 is quite low near the beginning and end of genes. Although elevated CG and CHG methylation are found within gene bodies, CHH and H3K9me2 remain low. Maize has much higher levels of CHG methylation within gene bodies than observed in Arabidopsis and this is partially attributable to the presence of transposons within introns for some maize genes. These transposons are associated with high levels of CHG methylation and H3K9me2 but do not appear to prevent transcriptional elongation. Although the general trend is for a strong depletion of H3K9me2 and CHG near the transcription start site there are some putative genes that have high levels of these chromatin modifications. This study provides a clear view of the relationship between DNA methylation and H3K9me2 in the maize genome and how the distribution of these modifications is shaped by the interplay of genes and transposons.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromatin Immunoprecipitation
Cluster Analysis
DNA Methylation*
DNA Transposable Elements
Epigenesis, Genetic
Evolution, Molecular
Gene Expression Profiling
Gene Expression Regulation, Plant
Genes, Plant
Genome, Plant*
Genome-Wide Association Study
High-Throughput Nucleotide Sequencing
Histones / metabolism*
Introns
Promoter Regions, Genetic
Transcription Initiation Site
Zea mays / genetics*
Zea mays / metabolism*

Substances

DNA Transposable Elements
Histones

Grants and funding

The research was supported by a grant from the National Science Foundation (IOS-1237931) to MWV and NMS. This work also used resources or cyberinfrastructure provided by iPlant Collaborative. The iPlant Collaborative is funded by a grant from the National Science Foundation (DBI-0735191; www.iplantcollaborative.org). Start-up funds from the University of Georgia and a research grant from the National Science Foundation (IOS-1339194) to RJS supported aspects of this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.