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Nat Plants. 2016 Apr 29;2(5):16058. doi: 10.1038/nplants.2016.58.

Unique cell-type-specific patterns of DNA methylation in the root meristem.

Author information

1
Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.
2
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.
3
Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
4
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia 6009, Australia.
5
Department of Biology, Duke University, Durham, North Carolina 27708, USA.
6
Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.
7
Howard Hughes Medical Institute, Duke University, Durham, North Carolina 27708, USA.
8
Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.

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.

PMID:
27243651
PMCID:
PMC4855458
DOI:
10.1038/nplants.2016.58
[Indexed for MEDLINE]
Free PMC Article

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