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Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth


The development of multicellular organisms relies on the coordinated control of cell divisions leading to proper patterning and growth1,2,3. The molecular mechanisms underlying pattern formation, particularly the regulation of formative cell divisions, remain poorly understood. In Arabidopsis, formative divisions generating the root ground tissue are controlled by SHORTROOT (SHR) and SCARECROW (SCR)4,5,6. Here we show, using cell-type-specific transcriptional effects of SHR and SCR combined with data from chromatin immunoprecipitation-based microarray experiments, that SHR regulates the spatiotemporal activation of specific genes involved in cell division. Coincident with the onset of a specific formative division, SHR and SCR directly activate a D-type cyclin; furthermore, altering the expression of this cyclin resulted in formative division defects. Our results indicate that proper pattern formation is achieved through transcriptional regulation of specific cell-cycle genes in a cell-type- and developmental-stage-specific context. Taken together, we provide evidence for a direct link between developmental regulators, specific components of the cell-cycle machinery and organ patterning.

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Figure 1: SHR and SCR regulate genes involved in formative cell divisions.
Figure 2: SHR directly activates transcription factors and a cell-cycle gene.
Figure 3: Spatiotemporal activation of CYCD6;1.
Figure 4: SHR and SCR activate cell-cycle genes for formative divisions.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

The National Center for Biotechnology Information Gene Expression Omnibus ( accession numbers for the array data discussed in this manuscript are GSE15876 and GSE21338.


  1. 1

    Lewis, J. From signals to patterns: space, time, and mathematics in developmental biology. Science 322, 399–403 (2008)

    ADS  MathSciNet  CAS  Article  Google Scholar 

  2. 2

    Herranz, H. & Milan, M. Signalling molecules, growth regulators and cell cycle control in Drosophila. Cell Cycle 7, 3335–3337 (2008)

    CAS  Article  Google Scholar 

  3. 3

    Blilou, I. et al. The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. Nature 433, 39–44 (2005)

    ADS  CAS  Article  Google Scholar 

  4. 4

    Di Laurenzio, L. et al. The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell 86, 423–433 (1996)

    CAS  Article  Google Scholar 

  5. 5

    Helariutta, Y. et al. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell 101, 555–567 (2000)

    CAS  Article  Google Scholar 

  6. 6

    Heidstra, R., Welch, D. & Scheres, B. Mosaic analyses using marked activation and deletion clones dissect Arabidopsis SCARECROW action in asymmetric cell division. Genes Dev. 18, 1964–1969 (2004)

    CAS  Article  Google Scholar 

  7. 7

    Foe, V. E. Mitotic domains reveal early commitment of cells in Drosophila embryos. Development 107, 1–22 (1989)

    CAS  PubMed  Google Scholar 

  8. 8

    Hartwell, L. H. & Kastan, M. B. Cell cycle control and cancer. Science 266, 1821–1828 (1994)

    ADS  CAS  Article  Google Scholar 

  9. 9

    Schiefelbein, J. Cell-fate specification in the epidermis: a common patterning mechanism in the root and shoot. Curr. Opin. Plant Biol. 6, 74–78 (2003)

    CAS  Article  Google Scholar 

  10. 10

    Benková, E. et al. Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell 115, 591–602 (2003)

    Article  Google Scholar 

  11. 11

    Aida, M. et al. The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell 119, 109–120 (2004)

    CAS  Article  Google Scholar 

  12. 12

    Wu, L. et al. The E2F1–3 transcription factors are essential for cellular proliferation. Nature 414, 457–462 (2001)

    ADS  CAS  Article  Google Scholar 

  13. 13

    Blilou, I. et al. The Arabidopsis HOBBIT gene encodes a CDC27 homolog that links the plant cell cycle to progression of cell differentiation. Genes Dev. 16, 2566–2575 (2002)

    CAS  Article  Google Scholar 

  14. 14

    Andersen, S. U. et al. Requirement of B2-type cyclin-dependent kinases for meristem integrity in Arabidopsis thaliana. Plant Cell 20, 88–100 (2008)

    CAS  Article  Google Scholar 

  15. 15

    Ebel, C., Mariconti, L. & Gruissem, W. Plant retinoblastoma homologues control nuclear proliferation in the female gametophyte. Nature 429, 776–780 (2004)

    ADS  CAS  Article  Google Scholar 

  16. 16

    Weigmann, K., Cohen, S. M. & Lehner, C. F. Cell cycle progression, growth and patterning in imaginal discs despite inhibition of cell division after inactivation of Drosophila Cdc2 kinase. Development 124, 3555–3563 (1997)

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17

    De Smet, I. et al. Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root. Science 322, 594–597 (2008)

    ADS  CAS  Article  Google Scholar 

  18. 18

    Benfey, P. N. et al. Root development in Arabidopsis: four mutants with dramatically altered root morphogenesis. Development 119, 57–70 (1993)

    CAS  PubMed  Google Scholar 

  19. 19

    Pysh, L. D., Wysocka-Diller, J. W., Camilleri, C., Bouchez, D. & Benfey, P. N. The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. Plant J. 18, 111–119 (1999)

    CAS  Article  Google Scholar 

  20. 20

    Nakajima, K., Sena, G., Nawy, T. & Benfey, P. N. Intercellular movement of the putative transcription factor SHR in root patterning. Nature 413, 307–311 (2001)

    ADS  CAS  Article  Google Scholar 

  21. 21

    Gallagher, K. L., Paquette, A. J., Nakajima, K. & Benfey, P. N. Mechanisms regulating SHORT-ROOT intercellular movement. Curr. Biol. 14, 1847–1851 (2004)

    CAS  Article  Google Scholar 

  22. 22

    Gallagher, K. L. & Benfey, P. N. Both the conserved GRAS domain and nuclear localization are required for SHORT-ROOT movement. Plant J. 57, 785–797 (2009)

    CAS  Article  Google Scholar 

  23. 23

    Sabatini, S., Heidstra, R., Wildwater, M. & Scheres, B. SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem. Genes Dev. 17, 354–358 (2003)

    CAS  Article  Google Scholar 

  24. 24

    Levesque, M. P. et al. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol. 4 e143 10.1371/journal.pbio.0040143 (2006)

    Article  PubMed  PubMed Central  Google Scholar 

  25. 25

    Cui, H. et al. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science 316, 421–425 (2007)

    ADS  CAS  Article  Google Scholar 

  26. 26

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

    ADS  CAS  Article  Google Scholar 

  27. 27

    Paquette, A. J. & Benfey, P. N. Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT. Plant Physiol. 138, 636–640 (2005)

    CAS  Article  Google Scholar 

  28. 28

    Menges, M., de Jager, S. M., Gruissem, W. & Murray, J. A. Global analysis of the core cell cycle regulators of Arabidopsis identifies novel genes, reveals multiple and highly specific profiles of expression and provides a coherent model for plant cell cycle control. Plant J. 41, 546–566 (2005)

    CAS  Article  Google Scholar 

  29. 29

    Brady, S. M. et al. A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318, 801–806 (2007)

    ADS  CAS  Article  Google Scholar 

  30. 30

    Haseloff, J. GFP variants for multispectral imaging of living cells. Methods Cell Biol. 58, 139–151 (1998)

    Article  Google Scholar 

  31. 31

    Fukaki, H. et al. Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana. Plant J. 14, 425–430 (1998)

    CAS  Article  Google Scholar 

  32. 32

    Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998)

    Article  Google Scholar 

  33. 33

    Bougourd, S., Marrison, J. & Haseloff, J. Technical advance: an aniline blue staining procedure for confocal microscopy and 3D imaging of normal and perturbed cellular phenotypes in mature Arabidopsis embryos. Plant J. 24, 543–550 (2000)

    CAS  Article  Google Scholar 

  34. 34

    Casamitjana-Martinez, E. et al. Root-specific CLE19 overexpression and the sol1/2 suppressors implicate a CLV-like pathway in the control of Arabidopsis root meristem maintenance. Curr. Biol. 13, 1435–1441 (2003)

    CAS  Article  Google Scholar 

  35. 35

    Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004)

    Article  Google Scholar 

  36. 36

    Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116–5121 (2001)

    ADS  CAS  Article  Google Scholar 

  37. 37

    Orlando, D. A., Brady, S. M., Koch, J. D., Dinneny, J. R. & Benfey, P. N. Manipulating large scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. Methods Mol. Biol. 553, 57–77 (2009)

    CAS  Article  Google Scholar 

  38. 38

    Busch, W. et al. Transcriptional control of a plant stem cell niche. Dev. Cell 18, 849–861 (2010)

    CAS  Article  Google Scholar 

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We thank D. Orlando and R. Twigg for generating the list of probes for the ChIP-array; J. Nieuwland, S. Maughan and C. Collins for construction of the CYCD6;1 reporter line and assistance in isolation of the cycd6;1 mutant; L. Sanz, F. Patell and S. Scofield for isolation of the cycd2;1 and cycd5;1 mutants; J. Dinneny, M. Noor and members of the Benfey laboratory for their comments on the manuscript. Funding to M.A.M.-R. is provided by the Ministerio de Ciencia y Innovacion (Spain). W.D. and J.A.H.M. were funded by a Biotechnology and Biological Sciences Research Council grant (BB/E022383) and the European Research Area in Plant Genomics network on Plant Stem Cells (BB/E024858). This work was funded by grants to P.N.B. from the NIH (RO1-GM043778 and P50-GM081883) and from the NSF (AT2010 0618304).

Author information




R.S., M.A.M.-R., J.A.H.M. and P.N.B. conceived and designed the experiments. H.C. and P.N.B. conceived and designed the ChIP-chip experiments. R.S., M.A.M.-R., W.B., J.M.V.N. and W.D. performed the experiments. R.S. and W.B. analysed the data. R.S., H.C., M.A.M.-R., T.V., S.M.B., J.A.H.M. and P.N.B. contributed reagents/materials/analysis tools. R.S., J.M.V.N. and P.N.B. wrote the paper.

Corresponding author

Correspondence to P. N. Benfey.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains legends for Supplementary Tables S1-S13, legends for Supplementary Movies 1-2, Supplementary References, Supplementary Figures S1-S18 with legends, and Supplementary Tables S1-S13. (PDF 9417 kb)

Supplementary Movie 1

This movie shows the in vivo periclinal divisions occurring in pSHR::SHR:GR shr-2-J0571 plants treated for 6 hours with Dex (see Supplementary Information file for full legend). (MOV 743 kb)

Supplementary Movie 2

This movie shows Col-0 and cycd6;1 seed germination. To monitor seed germination, images were taken with an infrared camera every 15’ for 48 hours (see Supplementary Information file for full legend). (MOV 2152 kb)

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Sozzani, R., Cui, H., Moreno-Risueno, M. et al. Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature 466, 128–132 (2010).

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