title: RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome.
abstract: The maize genome is relatively large (∼ 2.3 Gb) and has a complex organization of interspersed genes and transposable elements, which necessitates frequent boundaries between different types of chromatin. The examination of maize genes and conserved noncoding sequences revealed that many of these are flanked by regions of elevated asymmetric CHH (where H is A, C, or T) methylation (termed mCHH islands). These mCHH islands are quite short (∼ 100 bp), are enriched near active genes, and often occur at the edge of the transposon that is located nearest to genes. The analysis of DNA methylation in other sequence contexts and several chromatin modifications revealed that mCHH islands mark the transition from heterochromatin-associated modifications to euchromatin-associated modifications. The presence of an mCHH island is fairly consistent in several distinct tissues that were surveyed but shows some variation among different haplotypes. The presence of insertion/deletions in promoters often influences the presence and position of an mCHH island. The mCHH islands are dependent upon RNA-directed DNA methylation activities and are lost in mop1 and mop3 mutants, but the nearby genes rarely exhibit altered expression levels. Instead, loss of an mCHH island is often accompanied by additional loss of DNA methylation in CG and CHG contexts associated with heterochromatin in nearby transposons. This suggests that mCHH islands and RNA-directed DNA methylation near maize genes may act to preserve the silencing of transposons from activity of nearby genes.
authors.affiliation: Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108;
authors.forename: Qing
authors.initials: Q
authors.lastname: Li
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, GA 30602;
authors.forename: Jonathan I
authors.initials: JI
authors.lastname: Gent
authors.affiliation: Texas Advanced Computing Center, University of Texas at Austin, Austin, TX 78758;
authors.forename: Greg
authors.initials: G
authors.lastname: Zynda
authors.affiliation: Texas Advanced Computing Center, University of Texas at Austin, Austin, TX 78758;
authors.forename: Jawon
authors.initials: J
authors.lastname: Song
authors.affiliation: Department of Biology, Hamline University, Saint Paul, MN 55104;
authors.forename: Irina
authors.initials: I
authors.lastname: Makarevitch
authors.affiliation: Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108;
authors.forename: Cory D
authors.initials: CD
authors.lastname: Hirsch
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108;
authors.forename: Candice N
authors.initials: CN
authors.lastname: Hirsch
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, GA 30602;
authors.forename: R Kelly
authors.initials: RK
authors.lastname: Dawe
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306;
authors.forename: Thelma F
authors.initials: TF
authors.lastname: Madzima
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306;
authors.forename: Karen M
authors.initials: KM
authors.lastname: McGinnis
authors.affiliation: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907;
authors.forename: Damon
authors.initials: D
authors.lastname: Lisch
authors.affiliation: Department of Genetics, University of Georgia, Athens, GA 30602.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schmitz
authors.affiliation: Texas Advanced Computing Center, University of Texas at Austin, Austin, TX 78758;
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Vaughn
authors.affiliation: Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108; springer@umn.edu.
authors.forename: Nathan M
authors.initials: NM
authors.lastname: Springer
mesh_terms: D017124:Conserved Sequence / Q000235:genetics; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics; D022041:Euchromatin / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D005838:Genotype; D006570:Heterochromatin / Q000235:genetics*; D054643:INDEL Mutation / Q000235:genetics; D055029:Inverted Repeat Sequences / Q000235:genetics; D018749:RNA, Plant / Q000378:metabolism*; D024363:Transcription Initiation Site; D003313:Zea mays / Q000235:genetics*
chemical_list: D021901:DNA, Intergenic; D022041:Euchromatin; D006570:Heterochromatin; D018749:RNA, Plant
keywords: DNA methylation; RdDM; chromatin boundary; mCHH island; maize