Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine - PubMed (original) (raw)

Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine

Yunhai Li et al. Genome Res. 2006 Mar.

Abstract

Establishing transcriptional regulatory networks by analysis of gene expression data and promoter sequences shows great promise. We developed a novel promoter classification method using a Relevance Vector Machine (RVM) and Bayesian statistical principles to identify discriminatory features in the promoter sequences of genes that can correctly classify transcriptional responses. The method was applied to microarray data obtained from Arabidopsis seedlings treated with glucose or abscisic acid (ABA). Of those genes showing >2.5-fold changes in expression level, approximately 70% were correctly predicted as being up- or down-regulated (under 10-fold cross-validation), based on the presence or absence of a small set of discriminative promoter motifs. Many of these motifs have known regulatory functions in sugar- and ABA-mediated gene expression. One promoter motif that was not known to be involved in glucose-responsive gene expression was identified as the strongest classifier of glucose-up-regulated gene expression. We show it confers glucose-responsive gene expression in conjunction with another promoter motif, thus validating the classification method. We were able to establish a detailed model of glucose and ABA transcriptional regulatory networks and their interactions, which will help us to understand the mechanisms linking metabolism with growth in Arabidopsis. This study shows that machine learning strategies coupled to Bayesian statistical methods hold significant promise for identifying functionally significant promoter sequences.

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Figures

Figure 1.

Expression dynamics of glucose-responsive genes. (A) Venn diagrams showing the number of genes up-regulated by glucose at 2-h, 4-h, and 6-h time course points determined by microarray analyses. Here, 248 genes were up-regulated by glucose at all time points; 353 genes were induced by glucose at both 2 h and 4 h; 475 genes were up-regulated by glucose at both 4 h and 6 h; and 263 genes were glucose inducible at both 2 h and 6 h. (B) Venn diagrams showing the number of genes down-regulated by glucose at 2-h, 4-h, and 6-h time points determined by microarray analyses. Here, 347 genes were down-regulated by glucose at all time-course points; 416 genes were down-regulated by glucose at both 2 h and 4 h; 449 genes were repressed by glucose at both 4 h and 6 h; and 368 genes were glucose repressible at both 2 h and 6 h. (C) The expression profiles of glucose-inducible genes according to Quality Threshold clustering. Cluster number and time course are indicated. (D) The expression profiles of glucose-repressible genes according to Quality Threshold clustering. Cluster number and time course are indicated. (E) The expression profiles of heat-shock genes, starch metabolism, phenylpropanoid biosynthesis, N-, P-, and S-assimilation genes, and amino acid biosynthesis genes are shown.

Figure 2.

Glucose- and ABA-coregulated genes. (A) Functional classification of genes induced by both glucose and ABA. (B) Expression patterns of the set of 12 genes showing synergistic transcriptional responses to glucose and ABA. Expression patterns of the two genes encoding large subunits of AGPase (APL3 and AT2g21590) in response to glucose and ABA were indicated with a green line and black line, respectively. (C) Transcriptional responses of APL3:GUS promoter fusions to sugar and ABA in stable Arabidopsis transformants. Samples were taken from 7-d-old seedlings grown on the following media: 10 mM glucose + 90 mM mannitol (Mannitol), 100 mM glucose (Glucose), 10 mM glucose + 90 mM mannitol + 0.1 μM ABA (Mannitol + ABA), and 100 mM glucose + ABA (Glucose + ABA). The fold induction compared with the osmotic control (Mannitol) is given. Error bars represent the standard error from 10 independent transformants. (D) Response of the APL3 promoter to sugar and ABA in Arabidopsis protoplasts. Protoplasts were made from Col or isi3 7-d-old seedlings. Protoplasts were cultured in the following media: 400 mM mannitol, 400 mM glucose, 400 mM mannitol + 10 μM ABA and 400 mM glucose + 10 μM ABA. GUS activity was measured and normalized to Luciferase (Luc) activity expressed from the CaMV 35S promoter. The fold induction compared with the osmotic control of each genotype are given. Error bars represent the standard error of the mean from three samples.

Figure 3.

ROC (Receiver Operating Characteristic) curves of RVM performance in classifying glucose- and ABA-regulated genes. (A) The ROC curves of glucose-regulated genes show the proportion of true positives selected by the RVM versus false positives. The performance is shown by the area under the ROC curve. PLACE element features (blue line) and _k_-mer features (pink line). A random selection is shown by the green line. (B) The ROC curves of ABA-up-regulated genes show the proportion of true positives selected by the RVM versus false positives. The performance is shown by the area under the ROC curve. PLACE element features (blue line) and _k_-mer features (pink line). A random selection is shown by the green line.

Figure 4.

The TELO motif confers glucose-mediated transcriptional regulation. (A) Expression patterns of the glucose-up-regulated genes with promoters containing the TELO motif. (B) Sequences of the TELO4, TEF4, and TEF1TELO3 motifs. (C) Constructs containing the TELO4, TEF4, and TEF1TELO3 motifs in a –60 CaMV::GUS reporter vector are shown. An oligonucleotide tetramer of TELO (TELO4) and TEF (TEF4) motifs and a combined motif (TEF1TELO3) containing one TEF sequence and three TELO sequences were inserted upstream of the –60 CaMV::GUS reporter construct. (D,E,F) Histochemical analysis of GUS activity of TEF1TELO3::GUS transgenic plants in response to 3% glucose (D), 3% mannitol (E), and water (F) for 12 h. GUS activities in lateral root primordia are shown. (G) GUS activity of TEF4::GUS, TELO4::GUS, and TEF1TELO3::GUS transgenic plants. Protoplasts made from 7-d-old TEF4::GUS, TELO4::GUS, and TEF1TELO3::GUS transgenic plants were cultured in 400 mM glucose or 400 mM mannitol for 48 h before GUS activity was measured. Error bars represent the standard error of the mean from five samples. These transgenic lines were assayed at least three times.

References

1. Abe, H., Yamaguchi-Shinozaki, K., Urao, T., Iwasaki, T., Hosokawa, D., and Shinozaki, K. 1997. Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Plant Cell 9 1859–1868. - PMC - PubMed
1. Abe, H., Urao, T., Ito, T., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. 2003. Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15 63–78. - PMC - PubMed
1. Ahmad, M., Jarillo, J.A., and Cashmore, A.R. 1998. Chimeric proteins between cry1 and cry2 Arabidopsis blue light photoreceptors indicate overlapping functions and varying protein stability. Plant Cell 10 197–207. - PMC - PubMed
1. Arenas-Huertero, F., Arroyo, A., Zhou, L., Sheen, J., and Leon, P. 2000. Analysis of Arabidopsis glucose insensitive mutants, gin5 and gin6, reveals a central role of the plant hormone ABA in the regulation of plant vegetative development by sugar. Genes & Dev. 14 2085–2096. - PMC - PubMed
1. Beer, M.A. and Tavazoie, S. 2004. Predicting gene expression from sequence. Cell 117 185–198. - PubMed

Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine - PubMed (original) (raw)