Abstract
A system-wide understanding of gene regulation will provide deep insights into plant development and physiology. In this chapter we describe a threefold approach to identify the gene regulatory networks in Arabidopsis thaliana that function in a specific tissue or biological process. Since no single method is sufficient to establish comprehensive and high-confidence gene regulatory networks, we focus on the integration of three approaches. First, we describe an in silico prediction method of transcription factor–DNA binding, then an in vivo assay of transcription factor–DNA binding by yeast-1-hybrid and lastly the identification of co-expression clusters by transcription factor induction in planta. Each of these methods provides a unique tool to advance our understanding of gene regulation, and together provide a robust model for the generation of gene regulatory networks.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, De Smet I (2012) Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell 24:3859–3875. doi:10.1105/tpc.112.100776
Gene regulatory networks - methods and protocols. (2012) Eds. Deplancke B and Gheldof N. ISBN 978-1-61779-292-2
Rim Y, Huang L, Chu H, Han X, Cho WK, Jeon CO, Kim HJ, Hong J-C, Lucas WJ, Kim J-Y (2011) Analysis of Arabidopsis transcription factor families revealed extensive capacity for cell-to-cell movement as well as discrete trafficking patterns. Mol Cells 32:519–526. doi:10.1007/s10059-011-0135-2
Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJM, Benfey PN (2011) A stele-enriched gene regulatory network in the Arabidopsis root. Mol Syst Biol 7:1–9. doi:10.1038/msb.2010.114
Gubelmann C, Waszak SM, Isakova A, Holcombe W, Hens K, Iagovitina A, Feuz J-D, Raghav SK, Simicevic J, Deplancke B (2013) msb201338. Mol Syst Biol 9:1–18. doi:10.1038/msb.2013.38
Yamaguchi N, Winter CM, Wu M-F, Kwon CS, William DA, Wagner D (2014) Chromatin immunoprecipitation from Arabidopsis tissues. Arabidopsis Book 12:1–9. doi:10.1199/tab.0170
Brady SM, Orlando DA, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318:801–806. doi:10.1126/science.1146265
Sozzani R, Cui H, Moreno-Risueno MA, Busch W, Van Norman JM, Vernoux T, Brady SM, Dewitte W, Murray JAH, Benfey PN (2010) Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature 466:128–132. doi:10.1038/nature09143
Deplancke B (2004) A gateway-compatible yeast one-hybrid system. Genome Res 14:2093–2101. doi:10.1101/gr.2445504
Deplancke B, Vermeirssen V, Arda HE, Martinez NJ, Walhout AJM (2006) Gateway-compatible yeast one-hybrid screens. CSH Protoc. doi:10.1101/pdb.prot4590
Grant CE, Bailey TL, Noble WS (2011) FIMO: scanning for occurrences of a given motif. Bioinformatics 27:1017–1018. doi:10.1093/bioinformatics/btr064
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:W202–W208. doi:10.1093/nar/gkp335
Gaudinier A, Zhang L, Reece-Hoyes JS, Taylor-Teeples M, Pu L, Liu Z, Breton G, Pruneda-Paz JL, Kim D, Kay SA, Walhout AJM, Ware D, Brady SM (2011) Enhanced Y1H assays for Arabidopsis. Nat Methods 8:1053–1055. doi:10.1038/nmeth.1750
Clough SJ, Bent AF (1998) Floral dip: a simplified method forAgrobacterium‐mediated transformation of Arabidopsis thaliana. Plant J 16:735–743
Yamamoto YY, Yoshioka Y, Hyakumachi M, Obokata J (2011) Characteristics of core promoter types with respect to gene structure and expression in Arabidopsis thaliana. DNA Res 18:333–342. doi:10.1093/dnares/dsr020
Weirauch MT, Yang A, Albu M, Cote A, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano J-C, Galli M, Lewsey M, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJM, Bouget F-Y, Ratsch G, Larrondo LF, Ecker JR, Hughes TR. (2014) Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158(6):1431–43. doi: 10.1016/j.cell.2014.08.009
Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E (2011) AGRIS: the Arabidopsis gene regulatory information server, an update. Nucleic Acids Res 39:D1118–D1122. doi:10.1093/nar/gkq1120
Matys V (2006) TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34:D108–D110. doi:10.1093/nar/gkj143
Chai C, Xie Z, Grotewold E (2011) SELEX (Systematic Evolution of Ligands by EXponential Enrichment), as a powerful tool for deciphering the protein–DNA interaction space. In: Methods in molecular biology. Humana Press, Totowa, NJ, Eds. Ling Yuan and Sharyn E. Perry pp 249–258
Alexandrov NN, Troukhan ME, Brover VV, Tatarinova T, Flavell RB, Feldmann KA (2006) Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol Biol 60:69–85. doi:10.1007/s11103-005-2564-9
Lee J-Y, Colinas J, Wang JY, Mace D, Ohler U, Benfey PN (2006) Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc Natl Acad Sci U S A 103:6055–6060. doi:10.1073/pnas.0510607103
Coego A, Brizuela E, Castillejo P, Ruíz S, Koncz C, del Pozo JC, Piñeiro M, Jarillo JA, Paz-Ares J, León J, The TRANSPLANTA Consortium (2014) The TRANSPLANTA collection of Arabidopsis lines: a resource for functional analysis of transcription factors based on their conditional overexpression. Plant J 77:944–953. doi:10.1111/tpj.12443
Aoyama T, Chua N-H (1997) A glucocorticoid‐mediated transcriptional induction system in transgenic plants. Plant J 11:605–612. doi:10.1104/pp.110.154013
Acknowledgements
We gratefully acknowledge members of the Benfey lab for their comments on this chapter and Siobhan Brady for instruction on yeast-1-hybrid assays. Research in the Benfey lab is supported by funding from the National Institutes of Health, the National Science Foundation, and the Gordon and Betty Moore Foundation.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Sparks, E.E., Benfey, P.N. (2016). Identifying Gene Regulatory Networks in Arabidopsis by In Silico Prediction, Yeast-1-Hybrid, and Inducible Gene Profiling Assays. In: Caillaud, MC. (eds) Plant Cell Division. Methods in Molecular Biology, vol 1370. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3142-2_3
Download citation
DOI: https://doi.org/10.1007/978-1-4939-3142-2_3
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3141-5
Online ISBN: 978-1-4939-3142-2
eBook Packages: Springer Protocols