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.

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We thank K. Slotkin (Ohio State Univ., USA) and J.A.H. Murray (Univ. Cardiff, UK) for kindly providing DDM1–GFP seeds and ProCYCD5–GFP seeds, respectively. T.K. was supported by the Japan Society for the Promotion of Sciences Research Abroad Fellowship. T.S was supported by the Jean Rogerson Postgraduate Scholarship. This research was supported by grants from the National Science Foundation (MCB-1344299 to J.R.E and IOS-1021619 to P.N.B.), by the National Institutes of Health (GM R01-043778 to P.N.B.) and by the Gordon and Betty Moore Foundation (GBMF3034 to J.R.E and GBMF3405 to P.N.B.). R.L. was supported by the Australian Research Council (FT120100862). R.J.S. was supported by the National Institutes of Health (R00GM100000). J.R.E. and P.N.B. are investigators of the Howard Hughes Medical Institute.

Author information

Author notes

    • Taiji Kawakatsu
    • , Tim Stuart
    •  & Manuel Valdes

    These authors contributed equally to this work.


  1. Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • Taiji Kawakatsu
    • , Robert J. Schmitz
    •  & Joseph R. Ecker
  2. Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • Taiji Kawakatsu
    • , Robert J. Schmitz
    • , Joseph R. Nery
    • , Mark A. Urich
    • , Ryan Lister
    •  & Joseph R. Ecker
  3. Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan

    • Taiji Kawakatsu
  4. ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia 6009, Australia

    • Tim Stuart
    •  & Ryan Lister
  5. Department of Biology, Duke University, Durham, North Carolina 27708, USA

    • Manuel Valdes
    • , Natalie Breakfield
    • , Xinwei Han
    •  & Philip N. Benfey
  6. Department of Genetics, University of Georgia, Athens, Georgia 30602, USA

    • Robert J. Schmitz
  7. Howard Hughes Medical Institute, Duke University, Durham, North Carolina 27708, USA

    • Philip N. Benfey
  8. Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • Joseph R. Ecker


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P.N.B., J.R.E. and R.L. designed and supervised research. N.B., X.H. and M.V. collected cells. T.K., R.L., J.R.N. and M.A.U. conducted MethylC-seq experiments. R.L., J.R.N. and M.A.U. conducted RNA-seq experiments. T.K. and R.L. performed sequencing data processing. T.K., R.L., R.J.S. and T.S. performed statistical and bioinformatic analyses. R.J.S. performed imaging analyses. P.N.B., J.R.E., T.K., R.L. and T.S. prepared the manuscript.

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The authors declare no competing financial interests.

Corresponding authors

Correspondence to Ryan Lister or Philip N. Benfey or Joseph R. Ecker.

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