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

Abstract

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 (http://www.ncbi.nlm.nih.gov/geo/) accession numbers for the array data discussed in this manuscript are GSE15876 and GSE21338.

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Acknowledgements

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).

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Authors

Contributions

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). https://doi.org/10.1038/nature09143

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