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Plant Signal Behav. 2010 July; 5(7): 907–910.
PMCID: PMC3014545

NAC genes

Time-specific regulators of hormonal signaling in Arabidopsis


Environmental stresses on both animals and plants impose massive transcriptional perturbations. Successful adaptations to such stresses are being orchestrated by both activating and repressing effects of transcription factors on specific target genes. We have recently published a systematic characterization of members of the large NAC gene transcription factor family in the model weed Arabidopsis thaliana. Our analysis revealed interesting sub-groupings of the Arabidopsis NAC genes, relating structure and function. Here we present a meta-analysis revealing distinct temporal expression profiles of NAC genes upon stimuli with seven phytohormones. Our analysis could be a first indication of NAC-centered transcriptional networks, which coordinate timely hormonal signaling in plants.

Key words: Arabidopsis, NAC genes, hormonal signaling, transcription factor, network

Phytohormones play pivotal roles in many developmental and stress-related processes in plants.1,2 Adequate perception and adaptation to hormonal fluctuations are to a large extent governed by regulatory proteins, including transcription factors.3,4 In plants, NAC transcription factors constitute one of the largest transcription factor families with over 100 family members in Arabidopsis.5 Several NAC proteins have been reported to be involved in hormone-related processes during plant development and environmental stresses.69

To provide a comprehensive overview of hormone-inducible NAC genes a metaanalysis of NAC gene expression patterns was performed using genome-wide expression datasets at the AtGenExpress repository: (

This revealed prominent time- and hormone-specific regulation of NAC genes in response to hormone treatments applied at three different time-points by Goda et al.10 (Fig. 1). By unsupervised hierarchical clustering of 21 experiments (three time-points, seven hormones) arrays representing the same time-point clustered together; i.e., strong time-specific regulation of many NAC genes by all hormones tested (Clusters II–IV). Other NAC genes displayed time-independent and narrower hormonal induction (Clusters I and V). Overlapping regulation by several hormones of genes encoding regulatory proteins is in agreement with observations by Goda et al.10 supporting the notion on massive inter-connectivity between different hormonal signaling pathways sharing target genes at the transcriptional level.1012 However, and most importantly, all hormones tested not only regulate the expression of a large fraction of the NAC genes; hormonal regulation also displays distinct time-specificity. The AtGenExpress data, presented here, correlates with data available from the less extensive hormone expression study using the full-genome Arabidopsis TILING array13 (data not shown).

Figure 1
Expression and promoter analysis of Arabidopsis NAC genes. Eighty-nine ATH1 probe-sets matching Arabidopsis NAC genes were hierarchical clustered using Affymetrix GeneChip expression data from the AtGenExpress Consortium ( ...

For improved understanding of the observed expression patterns, we analyzed the 1 kb upstream promoter sequences of NAC gene clusters I–V using Promomer site: ( The analysis highlighted promoters of Cluster I genes to be significantly enriched in both ABA-responsive elements (ABRE), and cis-elements of GA repressed genes (GA_down)(p-values > 0.001 and 0.0001, respectively), as noted by Christianson et al.15 and in accordance with the antagonistic effects of ABA and GA.16 Interestingly, with the exception of At1g69490, this gene cluster corresponds to the ATAF subgroup of NAC genes defined by structure-based phylogenetic analysis,17 and could reflect evolution of the NAC gene family by gene duplication creating paralogous genes with a high degree of sequence similarity and functional redundancy. A consequence of redundancy among paralogous genes is a high degree of co-expression during development and stress perception in which they share functionality.18 It should be noted that apart from the significant hormonal-regulation of the 6 ATAF genes shown in Figure 1, McGrath et al.19 verified MeJA-induction of At3g15500 by qRT-PCR, and, moreover, showed that expression of At5g08790 (not present on the ATH1 GeneChip) was also induced by MeJA. Hence, both ABA and MeJA induce the entire ATAF subgroup. Another prominent co-expression cluster (Cluster II) contains NAC genes, which show early induction of expression by all hormone treatments. Surprisingly, early hormone-responsive NAC genes are not over-represented in any known hormone responsive elements. Neither are the promoters of NAC genes with expression induced late by most hormones tested (Cluster IV). Hormone-responsive NAC genes induced at 1 hr after hormone application (Cluster III), however, are significantly over-represented in both jasmonate-responsive elements (JRE) (p value > 0.005) and ethylene-responsive elements (ERE) (p > 0.005). The small cluster of ABA-only responsive genes (Cluster V) has an over-representation of JRE (p values > 0.001), whereas ABRE is not significantly over-represented. Finally, most NAC genes contain one or more NAC-binding sites (NACBS) in their 1 kb upstream promoter. In conclusion, three of five NAC clusters have significant over-representation of specific hormone-response elements in their promoters reflecting pronounced hormonal regulation of NAC gene expression.

To further investigate whether clustering of NAC gene expression in response to hormone-treatments is representative of overall NAC gene expression-based clustering, we used PRIMe software ( to analyze expression datasets involving the entire 1388 Arabidopsis ATH1 GeneChip arrays in the AtGenExpress project.21,22 This analysis identified 36 NAC genes, which correlate in their expression profile with one, two or three other NAC genes (Fig. 2). Again, Cluster I ATAF-like genes form a significant pattern with several interconnectivities representing co-expression. In addition to pronounced intra-cluster connectivities, members of this cluster connect with At5g39610 (NAC2/ORE1), also known to respond to hormonal exposures.7 Also, the CUC genes (At1g76420, At5g53950 and At3g15170) are co-expressed in accordance with their structural relationships.17 However, this is not reflected in the overall hormonal regulation due to significant differences in the time-dependence of induction by specific hormones. Altogether this illustrates that for the ATAF-like NAC genes, clustering based on hormone-induced expression profiles correlates with their overall expression perturbations during development and stress. However, the PRIMe analysis also reveals co-expression patterns not reflected in those resulting from hormone-treatments.

Figure 2
A NAC gene co-expression network built using PRIMe ( A stringent cut-off (0.6) was used to identify NAC co-expression profiles from 1388 Arabidopsis ATH1 array samples from the AtGenExpress Consortium ( ...

In summary, the time-specific expression patterns of many NAC genes in response to all hormones tested reflects an interesting ‘NACome’-mediated fine-tuning of hormonal perception, in which a set of early NAC hormonal signaling regulators (Cluster II) potentially regulates a secondary intermediate class of co-expressed NAC genes (Cluster III), that eventually targets a third class of late hormone-inducible NAC genes. The late hormone-inducible NAC genes seem to have a more narrow range of inducers (Cluster IV), than the early and intermediate hormone-inducible NAC genes. Previous studies have already shown that NAC proteins can regulate expression of the corresponding or other NAC genes.9,23 However, further studies of time-specific DNA-binding are needed to determine if NAC genes are direct targets of other NAC family members in hormonal-signaling.


This study was supported by the Danish Agency for Science (274-07-0173 and 09-064140/FTP).


abscisic acid
gibberelic acid



1. Asselbergh B, De Vleesschauwer D, Höfte M. Global switches and fine-tuning-ABA modulates plant pathogen defense. Mol Plant Microbe Interact. 2008;21:709–719. [PubMed]
2. Wolters H, Jurgens G. Survival of the flexible: hormonal growth control and adaptation in plant development. Nat Rev Genet. 2009;10:305–317. [PubMed]
3. Wu Y, Deng Z, Lai J, Zhang Y, Yang C, Yin B, et al. Dual function of Arabidopsis ATAF1 in abiotic and biotic stress responses. Cell Res. 2009;19:1279–1290. [PubMed]
4. Seo PJ, Park CM. A membrane-bound NAC transcription factor as an integrator of biotic and abiotic stress signals. Plant Signal Behav. 2010 In press. [PubMed]
5. Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science. 2000;290:2105–2110. [PubMed]
6. Fujita M, Fujita Y, Maruyama K, Seki M, Hiratsu K, Ohme-Takagi M, et al. A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. Plant J. 2004;39:863–876. [PubMed]
7. He XJ, Mu RL, Cao WH, Zhang ZG, Zhang JS, Chen SY. AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J. 2005;44:903–916. [PubMed]
8. Jensen MK, Hagedorn PH, de Torres-Zabala M, Grant MR, Rung JH, Collinge DB, et al. Transcriptional regulation by an NAC (NAM-ATAF1,2-CUC2) transcription factor attenuates ABA signalling for efficient basal defence towards Blumeria graminis f. sp. hordei in Arabidopsis. Plant J. 2008;56:867–880. [PubMed]
9. Xie Q, Frugis G, Colgan D, Chua NH. Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Genes Dev. 2000;14:3024–3036. [PubMed]
10. Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li W, et al. The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J. 2008;55:526–542. [PubMed]
11. Nakamura A, Nakajima N, Goda H, Shimada Y, Hayashi K, Nozaki H, et al. Arabidopsis Aux/IAA genes are involved in brassinosteroid-mediated growth responses in a manner dependent on organ type. Plant J. 2006;45:193–205. [PubMed]
12. Nemhauser JL, Hong F, Chory J. Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell. 2006;126:467–475. [PubMed]
13. Zeller G, Henz SR, Widmer CK, Sachsenberg T, Ratsch G, Weigel D, et al. Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J. 2009;58:1068–1082. [PubMed]
14. Bassel GW, Provart NJ. Gene expression analyses for elucidating mechanisms of hormonal action in plants. Methods Mol Biol. 2009;495:21–37. [PubMed]
15. Christianson JA, Dennis ES, Llewellyn DJ, Wilson IW. ATAF NAC transcription factors: Regulators of plant stress signaling. Plant Signal Behav. 2010;5:1–5. [PubMed]
16. Skriver K, Olsen FL, Rogers JC, Mundy J. Cis-acting DNA elements responsive to gibberellin and its antagonist abscisic acid. Proc Natl Acad Sci USA. 1991;88:7266–7270. [PubMed]
17. Jensen MK, Kjaersgaard T, Nielsen MM, Galberg P, Petersen K, O'Shea C, et al. The Arabidopsis thaliana NAC transcription factor family: structure-function relationships and determinants of ANAC019 stress signalling. Biochem J. 2010;426:183–196. [PubMed]
18. de Folter S, Busscher J, Colombo L, Losa A, Angenent GC. Transcript profiling of transcription factor genes during silique development in Arabidopsis. Plant Mol Biol. 2004;56:351–366. [PubMed]
19. McGrath KC, Dombrecht B, Manners JM, Schenk PM, Edgar CI, Maclean DJ, et al. Repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression. Plant Physiol. 2005;139:949–959. [PubMed]
20. Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, et al. PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biol. 2008;8:339–345. [PubMed]
21. Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, et al. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 2007;50:347–363. [PubMed]
22. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, et al. A gene expression map of Arabidopsis thaliana development. Nat Genet. 2005;37:501–506. [PubMed]
23. Vroemen CW, Mordhorst AP, Albrecht C, Kwaaitaal MA, de Vries SC. The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis. Plant Cell. 2003;15:1563–1577. [PubMed]
24. Wu Z, Irizarry RA. Preprocessing of oligonucleotide array data. Nat Biotechnol. 2004;22:656–658. [PubMed]
25. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:80. [PMC free article] [PubMed]
26. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 1998;95:14863–14868. [PubMed]

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