Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Chromatin organization and cell fate switch respond to positional information in Arabidopsis


Many types of plant cell retain their developmental plasticity and have the capacity to switch fate when exposed to a new source of positional information. In the root epidermis of Arabidopsis, cells differentiate in alternating files of hair cells and non-hair cells1,2, in response to positional information and the activity of the homoeodomain transcription factor GLABRA2 (GL2) in future non-hair cells3,4,5,6. Here we show by three-dimensional fluorescence in situ hybridization on intact root epidermal tissue that alternative states of chromatin organization around the GL2 locus are required to control position-dependent cell-type specification. When, as a result of an atypical cell division, a cell is displaced from a hair file into a non-hair file, it switches fate6. We show that during this event the chromatin state around the GL2 locus is not inherited, but is reorganized in the G1 phase of the cell cycle in response to local positional information. This ability to remodel chromatin organization may provide the basis for the plasticity in plant cell fate changes.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Cell-type-specific chromatin organization at the GL2 locus in meristematic epidermal nuclei.
Figure 2: FAS2 is required to control position-dependent cell-type specification.
Figure 3: Epidermal T clones show that chromatin state in the GL2 region is defined by position and not by cell lineage.
Figure 4: Chromatin state in the GL2 region is reset upon change in cell position.


  1. Dolan, L. et al. Clonal relationships and patterning in the root epidermis of Arabidopsis. Development 120, 2465–2474 (1994)

    CAS  Google Scholar 

  2. Galway, M. E. et al. The TTG gene is required to specify epidermal cell fate and cell patterning in the Arabidopsis root. Dev. Biol. 166, 740–754 (1994)

    CAS  Article  Google Scholar 

  3. Masucci, J. D. et al. The homeobox gene GLABRA2 is required for position-dependent cell differentiation in the root epidermis of Arabidopsis thaliana. Development 122, 1253–1260 (1996)

    CAS  PubMed  Google Scholar 

  4. Di Cristina, M. et al. The Arabidopsis Athb-10 (GLABRA2) is an HD-Zip protein required for regulation of root hair development. Plant J. 10, 393–402 (1996)

    CAS  Article  Google Scholar 

  5. Hung, C. Y. et al. A common position-dependent mechanism controls cell-type patterning and GLABRA2 regulation in the root and hypocotyl epidermis of Arabidopsis. Plant Physiol. 117, 73–84 (1998)

    CAS  Article  Google Scholar 

  6. Berger, F., Haseloff, J., Schiefelbein, J. & Dolan, L. Positional information in the root epidermis is defined during embryogenesis and acts in domains with strict boundaries. Curr. Biol. 8, 421–430 (1998)

    CAS  Article  Google Scholar 

  7. Lin, Y. & Schiefelbein, J. Embryonic control of epidermal cell patterning in the root and hypocotyl of Arabidopsis. Development 128, 3697–3705 (2001)

    CAS  PubMed  Google Scholar 

  8. Costa, S. & Dolan, L. Epidermal patterning genes are active during embryogenesis in Arabidopsis. Development 130, 2839–2901 (2003)

    Google Scholar 

  9. Kwak, S. H., Shen, R. & Schiefelbein, J. Positional signalling mediated by a receptor-like kinase in Arabidopsis. Science 307, 1111–1113 (2005)

    ADS  CAS  Article  Google Scholar 

  10. Lee, M. M. & Schiefelbein, J. WEREWOLF, a MYB-related protein in Arabidopsis, is a positional-dependent regulator of epidermal cell patterning. Cell 99, 473–483 (1999)

    CAS  Article  Google Scholar 

  11. Lee, M. M. & Schiefelbein, J. Cell pattern in the Arabidopsis root epidermis determined by lateral inhibition with feedback. Plant Cell 14, 611–618 (2002)

    CAS  Article  Google Scholar 

  12. Wada, T., Tachibana, T., Shimura, Y. & Okada, K. Epidermal cell differentiation in Arabidopsis determined by a Myb homolog, CPC. Science 277, 1113–1116 (1997)

    CAS  Article  Google Scholar 

  13. Wada, T. et al. Role of a positive regulator of root hair development, CAPRICE, in Arabidopsis root epidermal cell differentiation. Development 129, 5409–5419 (2002)

    CAS  Article  Google Scholar 

  14. Kaya, H. et al. FASCIATA genes for chromatin assembly factor-1 in Arabidopsis maintain the cellular organization of apical meristems. Cell 104, 131–142 (2001)

    CAS  Article  Google Scholar 

  15. Wolpert, L. Cell boundaries: knowing who to mix with and what to shout or whisper. Development 130, 4497–4500 (2003)

    CAS  Article  Google Scholar 

  16. Szymkowiak, E. J. & Sussex, I. M. What chimeras can tell us about plant development. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47, 351–376 (1996)

    Article  Google Scholar 

  17. Dolan, L. & Okada, K. Signalling in cell specification. Semin. Cell Dev. Biol. 10, 149–156 (1999)

    CAS  Article  Google Scholar 

  18. Kidner, C., Sundaresan, V., Roberts, K. & Dolan, L. Clonal analysis of the Arabidopsis root confirms that position, not lineage, determines cell fate. Planta 211, 191–199 (2000)

    CAS  Article  Google Scholar 

  19. Laux, T. The stem cell concept in plants: a matter of debate. Cell 113, 281–283 (2003)

    CAS  Article  Google Scholar 

Download references


We thank L. Dolan, G. Moore, C. Dean and M. Towers for discussion and advice. This work was funded by the BBSRC and the Gatsby Charitable Foundation.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Peter Shaw.

Ethics declarations

Competing interests

Reprints and permissions information is available at The authors declare no competing financial interests.

Supplementary information

Supplementary Figure 1

Schematic representation of the organisation of the Arabidopsis root epidermis. (DOC 192 kb)

Supplementary Figure 2

Close-ups of chromatin organisation at the GL2 locus in wild-type and cpc nuclei and scatter plots of FISH signal intensities measured on both. (DOC 394 kb)

Supplementary Figure 3

In wer mutant every cell of the meristematic root epidermis is in an open chromatin state in the GL2 region. (DOC 640 kb)

Supplementary Figure 4

The number of FISH signals detected indicates the cell cycle stage. (DOC 486 kb)

Supplementary Figure 5

Throughout mitosis the GL2 locus is accessible to FISH probes. (DOC 91 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Costa, S., Shaw, P. Chromatin organization and cell fate switch respond to positional information in Arabidopsis. Nature 439, 493–496 (2006).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing