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

Published

Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Kawakatsu, T; Stuart, T; Valdes, M; Breakfield, N; Schmitz, RJ; Nery, JR; Urich, MA; Han, X; Lister, R; Benfey, PN; Ecker, JR

Published Date

  • April 29, 2016

Published In

Volume / Issue

  • 2 / 5

Start / End Page

  • 16058 -

PubMed ID

  • 27243651

Pubmed Central ID

  • 27243651

Electronic International Standard Serial Number (EISSN)

  • 2055-0278

International Standard Serial Number (ISSN)

  • 2055-0278

Digital Object Identifier (DOI)

  • 10.1038/nplants.2016.58

Language

  • eng