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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

    & Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Rev. Genet. 11, 204–220 (2010).

  2. 2.

    & RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nature Rev. Genet. 15, 394–408 (2014).

  3. 3.

    et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153, 193–205 (2013).

  4. 4.

    et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nature Struct. Mol. Biol. 21, 64–72 (2014).

  5. 5.

    , & An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401, 157–161 (1999).

  6. 6.

    et al. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. eLife 4, e09343 (2015).

  7. 7.

    et al. Widespread dynamic DNA methylation in response to biotic stress. Proc. Natl Acad. Sci. USA 109, E2183–E2191 (2012).

  8. 8.

    et al. Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting. eLife 3, e03198 (2014).

  9. 9.

    et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, 461–472 (2009).

  10. 10.

    et al. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151, 194–205 (2012).

  11. 11.

    et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337, 1360–1364 (2012).

  12. 12.

    et al. Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461, 427–430 (2009).

  13. 13.

    et al. Bursts of retrotransposition reproduced in Arabidopsis. Nature 461, 423–426 (2009).

  14. 14.

    , , & Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis. EMBO Rep. 15, 446–452 (2014).

  15. 15.

    , , , & Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genet. 10, e1004785 (2014).

  16. 16.

    , , & Epigenetic differences between shoots and roots in Arabidopsis reveals tissue-specific regulation. Epigenetics 9, 236–242 (2014).

  17. 17.

    et al. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334, 369–373 (2011).

  18. 18.

    et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480, 245–249 (2011).

  19. 19.

    et al. Patterns of population epigenomic diversity. Nature 495, 193–198 (2013).

  20. 20.

    , , , & Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152, 352–364 (2013).

  21. 21.

    et al. The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21–22 nucleotide small interfering RNAs. Plant Physiol. 162, 116–131 (2013).

  22. 22.

    et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189–1201 (2006).

  23. 23.

    , , , & Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genet. 39, 61–69 (2007).

  24. 24.

    et al. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr. Biol. 15, 154–159 (2005).

  25. 25.

    et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2, E104 (2004).

  26. 26.

    et al. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120, 613–622 (2005).

  27. 27.

    et al. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nature Genet. 38, 721–725 (2006).

  28. 28.

    et al. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell 19, 1507–1521 (2007).

  29. 29.

    et al. The histone variant H2A.W defines heterochromatin and promotes chromatin condensation in Arabidopsis. Cell 158, 98–109 (2014).

  30. 30.

    et al. Genome-wide demethylation of Arabidopsis endosperm. Science 324, 1451–1454 (2009).

  31. 31.

    & Genetic ablation of root cap cells in Arabidopsis. Proc. Natl Acad. Sci. USA 96, 12941–12946 (1999).

  32. 32.

    et al. Root gravitropism requires lateral root cap and epidermal cells for transport and response to a mobile auxin signal. Nature Cell Biol. 7, 1057–1065 (2005).

  33. 33.

    et al. Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin. EMBO Rep. 10, 1015–1021 (2009).

  34. 34.

    et al. Cellular organisation of the Arabidopsis thaliana root. Development 119, 71–84 (1993).

  35. 35.

    & Fluorescence-activated cell sorting in plant developmental biology. Methods Mol. Biol. 655, 313–319 (2010).

  36. 36.

    et al. Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell 17, 1908–1925 (2005).

  37. 37.

    , & D-type cyclins control cell division and developmental rate during Arabidopsis seed development. J Exp. Bot. 63, 3571–3586 (2012).

  38. 38.

    et al. A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root. Genes Dev 14, 2938–2943 (2000).

  39. 39.

    et al. A gene expression map of the Arabidopsis root. Science 302, 1956–1960 (2003).

  40. 40.

    et al. Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc. Natl Acad. Sci. USA 103, 6055–6060 (2006).

  41. 41.

    & WEREWOLF, a MYB-related protein in Arabidopsis, is a position-dependent regulator of epidermal cell patterning. Cell 99, 473–483 (1999).

  42. 42.

    et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008).

  43. 43.

    et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68–73 (2011).

  44. 44.

    , , , & MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protoc. 10, 475–483 (2015).

  45. 45.

    et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523, 212–216 (2015).

  46. 46.

    , & ‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes. Trends Genet. 28, 583–585 (2012).

  47. 47.

    et al. High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome Res. 22, 163–176 (2012).

  48. 48.

    et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).

  49. 49.

    et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol.14, R36 (2013).

  50. 50.

    et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protoc. 7, 562–578 (2012).

Download references


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


  1. Search for Taiji Kawakatsu in:

  2. Search for Tim Stuart in:

  3. Search for Manuel Valdes in:

  4. Search for Natalie Breakfield in:

  5. Search for Robert J. Schmitz in:

  6. Search for Joseph R. Nery in:

  7. Search for Mark A. Urich in:

  8. Search for Xinwei Han in:

  9. Search for Ryan Lister in:

  10. Search for Philip N. Benfey in:

  11. Search for Joseph R. Ecker in:


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.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

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

Supplementary information

About this article

Publication history