title: Unique cell-type-specific patterns of DNA methylation in the root meristem.
abstract: DNA methylation is an epigenetic modification that differs between plant organs and tissues, but the extent of variation between cell types is not known. Here, we report single-base-resolution whole-genome DNA methylomes, mRNA transcriptomes and small RNA transcriptomes for six cell populations covering the major cell types of the Arabidopsis root meristem. We identify widespread cell-type-specific patterns of DNA methylation, especially in the CHH sequence context, where H is A, C or T. The genome of the columella root cap is the most highly methylated Arabidopsis cell characterized so far. It is hypermethylated within transposable elements (TEs), accompanied by increased abundance of transcripts encoding RNA-directed DNA methylation (RdDM) pathway components and 24-nt small RNAs (smRNAs). The absence of the nucleosome remodeller DECREASED DNA METHYLATION 1 (DDM1), required for maintenance of DNA methylation, and low abundance of histone transcripts involved in heterochromatin formation suggests that a loss of heterochromatin may occur in the columella, thus allowing access of RdDM factors to the whole genome, and producing an excess of 24-nt smRNAs in this tissue. Together, these maps provide new insights into the epigenomic diversity that exists between distinct plant somatic cell types.
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.|Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.|Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Taiji
authors.initials: T
authors.lastname: Kawakatsu
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia 6009, Australia.
authors.forename: Tim
authors.identifier: 0000-0002-3044-0897
authors.initials: T
authors.lastname: Stuart
authors.affiliation: Department of Biology, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Manuel
authors.initials: M
authors.lastname: Valdes
authors.affiliation: Department of Biology, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Natalie
authors.identifier: 0000-0001-8517-885X
authors.initials: N
authors.lastname: Breakfield
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.|Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.|Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schmitz
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Nery
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Urich
authors.affiliation: Department of Biology, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Xinwei
authors.identifier: 0000-0003-3930-8427
authors.initials: X
authors.lastname: Han
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.|ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia 6009, Australia.
authors.forename: Ryan
authors.initials: R
authors.lastname: Lister
authors.affiliation: Department of Biology, Duke University, Durham, North Carolina 27708, USA.|Howard Hughes Medical Institute, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Philip N
authors.initials: PN
authors.lastname: Benfey
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.|Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.|Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D018519:Meristem / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D010940:Plant Proteins