Table III.
Promoter motifs from genes differentially regulated by both HL conditions
| Clusters and Motifs | Genes | Motif Name | Motif Function |
|---|---|---|---|
| HL-induced genes | |||
| CTrACCGTCC | 7 /15 (0.98) | A box/MBS | Cis-acting regulatory element, MYB-binding site |
| nAmGTTGGyr | 9 /15 (0.85) | CAAT box | Common cis-acting promoter element |
| CTATCT | 7 /15 (0.8) | Sbp-CMA1 | Module involved in light response |
| ATCCGACGTC | 3 /15 (0.99) | – | Unknown |
| AGTAACyA | 8 /15 (0.8) | – | Unknown |
| HL-repressed genes | |||
| AAGAAGAAGA | 23 /77 (0.8) | TCA element | Cis-acting element involved in SA responsiveness |
| CGTnTC | 18 /77 (0.8) | ABA response element (ABRE) | Cis-acting element involved in ABA responsiveness |
| CwTCTTCwTC | 27 /77 (0.8) | – | Unknown |
| CAAAGCAA | 21 /77 (0.8) | – | Unknown |
| fHL-induced genes | |||
| CTTCCn | 7 /28 (0.8) | G box | Cis-acting element involved in light responsiveness |
| nACGTGTmmC | 13 /28 (0.9) | ABRE | Cis-acting element involved in ABA responsiveness |
| CAmmCACmAm | 13 /28 (0.8) | – | Unknown |
| WCTyCmGATT | 13 /28 (0.8) | – | Unknown |
| fHL-repressed genes | |||
| ATAAATAAAA | 13 /28 (0.8) | TATA box | Core promoter element −30 of transcription start |
| GTCTCn | 10 /28 (0.8) | AuxRE | Part of auxin response element |
| CACTTwCC | 17 /28 (0.8) | – | Unknown |
| HL- plus fHL-induced genes | |||
| WTCTCCTTCs | 7 /14 (0.8) | TCCC motif | Part of light-responsive element (LRE) |
| GAAACT | 7 /14 (0.8) | Heat shock element (HSE) AE box | Heat stress response, part of LRE |
| CTTCTC | 9 /14 (0.8) | HSE | Heat stress response |
| TCGGATTCGT | 3 /14 (0.99) | – | Unknown |
| HL- plus fHL-repressed genes | |||
| TAAATAAAnm | 11 /34 (0.8) | 1 box | Part of LRE core promoter element |
| TCTTCTTC | 11 /34 (0.95) | sbpCMA1a | Part of LRE |
| ACCATA | 12 /34 (0.8) | ACA-motif | Part of LRE |
Promoter sequences (500 bp) for genes coregulated by two HL experiments were obtained from The Institute for Genome Research (ftp://www.tigr.org) and searched for overrepresented 6- to 10-motifs by a motif sampler (Thijs et al., 2001). Nos. represent the amount of promoters out of the total amount of promoters analyzed per cluster. Nos. in parentheses represent the probability score of that motif; the closer this score is to 1 the closer the motif resembles the motif model; >0.8 is considered significant. The letters other than A, C, G, and T are degenerate symbols. They represent a possible combination of two letters: A-T = W, A-C = M, A-G = R, C-G = S, C-T = Y, G-T = K, and n can be A, C, G, or T. The returned overrepresented motifs were compared to known plant motifs available from the PlantCARE database to determine function. HL, 1,000 μmol m−2 s−1; fHL, 1,000 μmol m−2 s−1 infrated filtered light. A list of genes containing each promoter motif is provided in the supplemental data.