Skip to main content

Thank you for visiting nature.com. 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.

An Arabidopsis gene regulatory network for secondary cell wall synthesis

Nature volume 517, pages 571–575 (2015)Cite this article

Subjects

Abstract

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein–DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.

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

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Regulators of xylem development and secondary cell wall biosynthesis.
Figure 2: E2Fc represses secondary cell wall gene biosynthesis.
Figure 3: Tissue-specific VND7 regulation and VND7 targets.
Figure 4: Multiple transcription factors bind the CESA4 promoter.
Figure 5: The xylem-specific gene regulatory network is responsive to high salinity and iron deprivation.

References

  1. Brown, D. M., Zeef, L. A. H., Ellis, J., Goodacre, R. & Turner, S. R. Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17, 2281–2295 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Persson, S., Wei, H., Milne, J., Page, G. P. & Somerville, C. R. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc. Natl Acad. Sci. USA 102, 8633–8638 (2005)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  3. Carlsbecker, A. et al. Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate. Nature 465, 316–321 (2010)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  4. Mitsuda, N., Seki, M., Shinozaki, K. & Ohme-Takagi, M. The NAC transcription factors NST1 and NST2 of Arabidopsis regulate secondary wall thickenings and are required for anther dehiscence. Plant Cell 17, 2993–3006 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  ADS  CAS  PubMed  Google Scholar 

  6. Zhong, R., Lee, C., Zhou, J., McCarthy, R. L. & Ye, Z.-H. A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell 20, 2763–2782 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Gaudinier, A. et al. Enhanced Y1H assays for Arabidopsis. Nature Methods 8, 1053–1055 (2011)

    Article  CAS  PubMed  Google Scholar 

  8. Kim, W.-C., Ko, J.-H. & Han, K.-H. Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis. Plant Mol. Biol. 78, 489–501 (2012)

    Article  CAS  PubMed  Google Scholar 

  9. Yamaguchi, M. et al. VASCULAR-RELATED NAC-DOMAIN 7 directly regulates the expression of a broad range of genes for xylem vessel formation. Plant J. 66, 579–590 (2011)

    Article  CAS  PubMed  Google Scholar 

  10. Zhou, J., Lee, C., Zhong, R. & Ye, Z. H. MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis. Plant Cell 21, 248–266 (2009)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Hussey, S. G., Mizrachi, E., Creux, N. M. & Myburg, A. A. Navigating the transcriptional roadmap regulating plant secondary cell wall deposition. Front. Plant Sci. 4, 325 (2013)

    Article  PubMed  PubMed Central  Google Scholar 

  12. Walhout, A. J. M. What does biologically meaningful mean? A perspective on gene regulatory network validation. Genome Biol. 12, 109 (2011)

    Article  PubMed  PubMed Central  Google Scholar 

  13. Kim, W.-C., Kim, J.-Y., Ko, J.-H., Kang, H. & Han, K.-H. Identification of direct targets of transcription factor MYB46 provides insights into the transcriptional regulation of secondary wall biosynthesis. Plant Mol. Biol. 85, 589–599 (2014)

    Article  CAS  PubMed  Google Scholar 

  14. Ahnert, S. E. Power graph compression reveals dominant relationships in genetic transcription networks. Mol. Biosyst. 9, 2681–2685 (2013)

    Article  CAS  PubMed  Google Scholar 

  15. Kim, W.-C. et al. MYB46 directly regulates the gene expression of secondary wall-associated cellulose synthases in Arabidopsis. Plant J. 73, 26–36 (2013)

    Article  CAS  PubMed  Google Scholar 

  16. del Pozo, J. C., Diaz-Trivino, S., Cisneros, N. & Gutierrez, C. The balance between cell division and endoreplication depends on E2FC-DPB, transcription factors regulated by the ubiquitin-SCFSKP2A pathway in Arabidopsis. Plant Cell 18, 2224–2235 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. del Pozo, J. C., Boniotti, M. B. & Gutierrez, C. Arabidopsis E2Fc functions in cell division and is degraded by the ubiquitin-SCFAtSKP2 pathway in response to light. Plant Cell 14, 3057–3071 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. de Jager, S. M., Menges, M., Bauer, U. M. & Murray, J. A. H. Arabidopsis E2F1 binds a sequence present in the promoter of S-phase-regulated gene AtCDC6 and is a member of a multigene family with differential activities. Plant Mol. Biol. 47, 555–568 (2001)

    Article  CAS  PubMed  Google Scholar 

  19. Mariconti, L. et al. The E2F family of transcription factors from Arabidopsis thaliana: novel and conserved components of the retinoblastoma/E2F pathway in plants. J. Biol. Chem. 277, 9911–9919 (2002)

    Article  CAS  PubMed  Google Scholar 

  20. Kosugi, S. & Ohashi, Y. Interaction of the Arabidopsis E2F and DP proteins confers their concomitant nuclear translocation and transactivation. Plant Physiol. 128, 833–843 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. de Jager, S. et al. Dissecting regulatory pathways of G1/S control in Arabidopsis: common and distinct targets of CYCD3;1, E2Fa and E2Fc. Plant Mol. Biol. 71, 345–365 (2009)

    Article  CAS  PubMed  Google Scholar 

  22. Heckmann, S. et al. The E2F transcription factor family regulates CENH3 expression in Arabidopsis thaliana. Plant J. 68, 646–656 (2011)

    Article  CAS  PubMed  Google Scholar 

  23. del Pozo, J. C., Diaz-Trivino, S., Cisneros, N. & Gutierrez, C. The E2FC-DPB transcription factor controls cell division, endoreplication and lateral root formation in a SCFSKP2A-dependent manner. Plant Signal. Behav. 2, 273–274 (2007)

    Article  PubMed  PubMed Central  Google Scholar 

  24. Yamaguchi, M. et al. VND-INTERACTING2, a NAC domain transcription factor, negatively regulates xylem vessel formation in Arabidopsis. Plant Cell 22, 1249–1263 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Yamaguchi, M. et al. VASCULAR-RELATED NAC-DOMAIN6 (VND6) and VND7 effectively induce transdifferentiation into xylem vessel elements under control of an induction system. Plant Physiol. 153, 906–914 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Wenkel, S., Emery, J., Hou, B.-H., Evans, M. M. S. & Barton, M. K. A feedback regulatory module formed by LITTLE ZIPPER and HD-ZIPIII genes. Plant Cell 19, 3379–3390 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Zhong, R. & Ye, Z.-H. MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes. Plant Cell Physiol. 53, 368–380 (2012)

    Article  CAS  PubMed  Google Scholar 

  28. Ohashi-Ito, K., Oda, Y. & Fukuda, H. Arabidopsis VASCULAR-RELATED NAC-DOMAIN6 directly regulates the genes that govern programmed cell death and secondary wall formation during xylem differentiation. Plant Cell 22, 3461–3473 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Pyo, H., Demura, T. & Fukuda, H. TERE; a novel cis-element responsible for a coordinated expression of genes related to programmed cell death and secondary wall formation during differentiation of tracheary elements. Plant J. 51, 955–965 (2007)

    Article  CAS  PubMed  Google Scholar 

  30. Dinneny, J. R. et al. Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320, 942–945 (2008)

    Article  ADS  CAS  PubMed  Google Scholar 

  31. Iyer-Pascuzzi, A. S. et al. Cell identity regulators link development and stress responses in the Arabidopsis root. Dev. Cell 21, 770–782 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Gifford, M. L., Dean, A., Gutierrez, R. A., Coruzzi, G. M. & Birnbaum, K. D. Cell-specific nitrogen responses mediate developmental plasticity. Proc. Natl Acad. Sci. USA 105, 803–808 (2008)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  33. Brady, S. M. et al. A stele-enriched gene regulatory network in the Arabidopsis root. Mol. Syst. Biol. 7, 459 (2011)

    Article  PubMed  PubMed Central  Google Scholar 

  34. Gong, W. et al. Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol. 135, 773–782 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Paz-Ares, J. & The REGIA Consortium. REGIA, an EU project on functional genomics of transcription factors from Arabidopsis thaliana. Comp. Funct. Genomics 3, 102–108 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Underwood, B. A., Vanderhaeghen, R., Whitford, R., Town, C. D. & Hilson, P. Simultaneous high-throughput recombinational cloning of open reading frames in closed and open configurations. Plant Biotechnol. J. 4, 317–324 (2006)

    Article  CAS  PubMed  Google Scholar 

  37. Yamada, K., Lim, J., Dale, J. & Chen, H. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302, 842–846 (2003)

    Article  ADS  CAS  PubMed  Google Scholar 

  38. Pruneda-Paz, J. L., Breton, G., Para, A. & Kay, S. A. A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science 323, 1481–1485 (2009)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  39. Kubo, M. et al. Transcription switches for protoxylem and metaxylem vessel formation. Genes Dev. 19, 1855–1860 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Hawker, N. P. & Bowman, J. L. Roles for class III HD-Zip and KANADI genes in Arabidopsis root development. Plant Physiol. 135, 2261–2270 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Updegraff, D. Semimicro determination of cellulose in biological materials. Anal. Biochem. 32, 420–424 (1969)

    Article  CAS  PubMed  Google Scholar 

  42. Scott, T. A. & Melvin, E. H. Determination of dextran with anthrone. Anal. Chem. 25, 1656–1661 (1953)

    Article  CAS  Google Scholar 

  43. Liu, Y., Burch-Smith, T., Schiff, M., Feng, S. & Dinesh-Kumar, S. P. Molecular chaperone Hsp90 associates with resistance protein N and its signaling proteins SGT1 and Rar1 to modulate an innate immune response in plants. J. Biol. Chem. 279, 2101–2108 (2004)

    Article  CAS  PubMed  Google Scholar 

  44. Voinnet, O., Rivas, S., Mestre, P. & Baulcombe, D. An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus. Plant J. 33, 949–956 (2003)

    Article  CAS  PubMed  Google Scholar 

  45. Walley, J. W. et al. Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. PLoS Genet. 3, e172 (2007)

    Article  PubMed Central  CAS  Google Scholar 

  46. Nusinow, D. A. et al. The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature 475, 398–402 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Pearson, R. D. et al. puma: a Bioconductor package for propagating uncertainty in microarray analysis. BMC Bioinformatics 10, 211 (2009)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  48. Mordelet, F. & Vert, J.-P. SIRENE: supervised inference of regulatory networks. Bioinformatics 24, i76–i82 (2008)

    Article  PubMed  Google Scholar 

  49. Huynh-Thu, V. A., Irrthum, A., Wehenkel, L. & Geurts, P. Inferring regulatory networks from expression data using tree-based methods. PLoS ONE 5, e12776 (2010)

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  50. Greenfield, A., Madar, A., Ostrer, H. & Bonneau, R. DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models. PLoS ONE 5, e13397 (2010)

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  51. Haury, A.-C., Mordelet, F., Vera-Licona, P. & Vert, J.-P. TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. BMC Syst. Biol. 6, 145 (2012)

    Article  PubMed  PubMed Central  Google Scholar 

  52. Küffner, R., Petri, T., Tavakkolkhah, P., Windhager, L. & Zimmer, R. Inferring gene regulatory networks by ANOVA. Bioinformatics 28, 1376–1382 (2012)

    Article  PubMed  CAS  Google Scholar 

  53. Marbach, D. et al. Wisdom of crowds for robust gene network inference. Nature Methods 9, 796–804 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank M. Tierney (University of Vermont) for 35S::GFP seeds, T. Demura for VND7 resources, M.K. Barton for REV:GR seeds, E.P. Spalding for advice on manuscript revision, and C. Gutierrez for E2Fc RNAi and E2Fc N-terminal deletion overexpressor seeds and useful discussion. This research was supported by the Office of Science (BER) Department of Energy Grant DE-FG02-08ER64700DE (to S.P.H. and S.A.K.), National Institute of General Medical Sciences of the National Institutes of Health under award numbers RO1GM056006 and RC2GM092412 (to S.A.K.), National Institute of Health (R01GM107311) and National Science Foundation (IOS-1036491 and IOS-1352478) to K.D., USDA CRIS 1907-21000-030 to D.W. and L.F., a Royal Society UK Fellowship (to S.E.A.), and UC Davis Startup Funds and a Hellman Fellowship (to S.M.B).

Author information

Author notes

  1. L. Lin, G. Breton & S. A. Kay

    Present address: Present addresses: Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA (L.L.); Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA (G.B.); Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089, USA (S.A.K.).,

  2. M. Taylor-Teeples, L. Lin and M. de Lucas: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA,

    M. Taylor-Teeples, M. de Lucas, G. Turco, T. W. Toal, A. Gaudinier, C. Wang, K. Dehesh & S. M. Brady

  2. Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA,

    M. Taylor-Teeples, M. de Lucas, G. Turco, T. W. Toal, A. Gaudinier, A. Tsoukalas, I. Tagkopoulos & S. M. Brady

  3. Biology Department, University of Massachusetts, Amherst, 01003, Massachusetts, USA

    L. Lin, N. F. Young, G. M. Trabucco, M. T. Veling, R. Lamothe, P. P. Handakumbura & S. P. Hazen

  4. Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, 94720, California, USA

    G. Xiong & M. Pauly

  5. Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, California 95616, USA,

    J. Corwin & D. J. Kliebenstein

  6. Department of Computer Science, University of California Davis, One Shields Avenue, Davis, California 95616, USA,

    A. Tsoukalas & I. Tagkopoulos

  7. Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, New York, USA

    L. Zhang & D. Ware

  8. US Department of Agriculture, Agricultural Research Service, Ithaca, 14853, New York, USA

    D. Ware

  9. Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, 92093, California, USA

    G. Breton, J. L. Pruneda-Paz & S. A. Kay

  10. Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK,

    S. E. Ahnert

Authors
  1. M. Taylor-Teeples
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. L. Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. de Lucas
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. G. Turco
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. T. W. Toal
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. A. Gaudinier
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. N. F. Young
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. G. M. Trabucco
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. M. T. Veling
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. R. Lamothe
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. P. P. Handakumbura
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. G. Xiong
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. C. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. J. Corwin
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. A. Tsoukalas
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. L. Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. D. Ware
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. M. Pauly
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. D. J. Kliebenstein
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. K. Dehesh
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. I. Tagkopoulos
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. G. Breton
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. J. L. Pruneda-Paz
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. S. E. Ahnert
    View author publications

    You can also search for this author in PubMed Google Scholar

  25. S. A. Kay
    View author publications

    You can also search for this author in PubMed Google Scholar

  26. S. P. Hazen
    View author publications

    You can also search for this author in PubMed Google Scholar

  27. S. M. Brady
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

M.T.-T., L.L. and M.d.L. contributed equally to this work. T.W.T. and A.G. contributed equally to this work. S.M.B. and S.P.H. contributed equally to this work. M.T.-T., L.L., M.d.L., S.M.B., and S.P.H. designed the research. M.T.-T., L.L., M.d.L., A.G., G.X., N.F.Y., G.M.T., M.T.V., R.L., P.P.H., C.W., and K.D. performed the research. M.T.-T., L.L., G.T., T.W.T., N.T., J.C., M.P., D.K., I.T., S.E.A., S.M.B. and S.P.H. analysed the data. L.Z., D.W., G.B., J.L.P.-P., and S.A.K. contributed new reagents/analytic tools. M.T.-T., L.L., G.M.T., S.M.B. and S.P.H. wrote the article. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to S. P. Hazen or S. M. Brady.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Number of novel and previously described protein–DNA interactions and transcription factors involved in secondary cell wall biosynthesis and xylem development.

a, b, Venn diagrams of overlap between previously reported19 interactions (a) or transcription factors (b) and those of the xylem-specific gene regulatory network. *Includes genes that were not included in the yeast one hybrid screen.

Extended Data Figure 2 Activation or repression of VND7 by E2Fc is dynamic and dose-dependent.

a, Intensity of LUC bioluminescence quantified using Andor Solis image analysis software. Data are means ± s.d. (n = 20). Asterisks denote significance at P < 0.05 determined by Student’s t-test. b, Quantitative PCR with reverse transcription of E2Fc and VND7 transcripts in ΔN-E2Fc (E2Fc overexpressor line lacking the N-terminal domain) expressing plants versus Col-0 control. Red dashed line marks the point at which VND7 is unchanged compared to control. Each data point is an individual biological replicate with 3 technical replicates. c, 3-week-old tobacco leaves were infiltrated with the p19 silencing inhibitor and either the reporter VND7p::GUS or VND7p::GUS and either 35S::E2Fc::MYC or 35S::RBR::GFP, or both. Extracted protein was then used in a quantitative MUG fluorescent assay, where relative fluorescence was measured 60 min after incubation with substrate. Data are means ± s.d., n = 3.

Extended Data Figure 3 Binding of NST2 and SND1 to fragments of CESA7, CESA8, and KOR promoters.

a–f, Electrophoretic mobility shift assays showing NST2 (a–d) and SND1 (e–f) protein specifically binds the promoters of cellulose-associated genes. Probe was incubated in the absence or presence of GST or GST:SND1 protein extracts. The arrowheads indicate the specific protein–DNA complexes, while arrows indicate free probe.

Extended Data Figure 4 Sub-networks of network genes differentially expressed in response to iron deprivation of high salinity.

a, b, Sub-network of genes with q values of ≤ 0.01 and whose fold change between mean expression values was ≥ 1.5 in either direction in iron deprivation (a) or high NaCl (b) stress microarray data set. Nodes are coloured according to in-degree as shown on scale bars below sub-networks. Transcription factors with the highest in-degree are labelled and indicated with a black circle.

Extended Data Figure 5 The reconstructed gene regulatory consensus network based on analysis of the iron-deprivation expression data set by different network inference methods.

a, Unsupervised; b, supervised in the first pass; c, supervised after the validated two connections have been added in the training set. Edge transparency denotes P ≤ 0.06 for the Pearson correlation coefficient (PCC); edge width is proportional to PCC; edge value corresponds to the total edge score; a greater value corresponds to a more significant score. Yellow and red nodes correspond to transcription factor and target gene nodes, respectively; black and blue edges denote Y1H-derived and inferred interactions, respectively.

Extended Data Figure 6 Iron deprivation and NaCl stress influences lignin and phenylpropanoid biosynthesis associated gene expression.

a, No change was observed in the expression of 4CL1::GFP in 4 days after imbibition (DAI) roots transferred to a control media (left, n = 4) or media with 140 mM NaCl for 48 h (right, n = 4). b, Increased fuchsin staining of xylem cells as well as of cell walls of non-vascular cells in 4 DAI roots transferred to a control media (left) or media with an iron chelator for 72 h (right). c, No change was observed in the expression of VND7::YFP in 4 DAI roots transferred to a control media (left, n = 4) or media with an iron chelator for 72 h (right, n = 5).

Extended Data Figure 7 The reconstructed gene regulatory consensus network based on analysis of the salt-stress expression data set by different network inference methods.

a, Unsupervised; b, supervised in the first pass; c, supervised after the validated two connections have been added in the training set. Edge transparency denotes P ≤ 0.06 for the Pearson correlation coefficient (PCC); edge width is proportional to PCC; edge value corresponds to the total edge score; a greater value corresponds to a more significant score. Yellow and red nodes correspond to transcription factor and target gene nodes, respectively; black and blue edges denote Y1H-derived and inferred interactions, respectively.

Extended Data Figure 8 Schematic diagram of dual-luciferase reporter vector development.

a, Three distinct donor vectors harbouring either the transcription factor, VP64 activation domain fused to the 35S minimal promoter, or a promoter fragment. b, The dual reporter vector, pLAH-LARm, is then recombined with the three donor vectors to generate the single reporter vector (c).

Supplementary information

Supplementary information

This zipped file contains Supplementary Tables 1-10 and a Supplementary Guide containing full table legends. (ZIP 424 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Taylor-Teeples, M., Lin, L., de Lucas, M. et al. An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature 517, 571–575 (2015). https://doi.org/10.1038/nature14099

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature14099

This article is cited by

Comments

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.

Search

Advanced search

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