Table 4.
Summary of Transcriptional Regulation of Target Genes (Table 2) and Transcription Factor Genes (Table 3). The Table Represents the Number of Response Elements Present in the Promoter Region of Differently Expressed Cold/Light (C/L) or Cold/Dark (C/D) or Dark (D)-Responsive Genes. Promoter Analysis Was Performed within 500 bps Upstream of Transcription Start Site using a Genomatix™ and Athena Programs. Response Elements that Are More than 90% Same within a Group of Expressed Genes are underlined According to Genomatix Gene2Promoter Analysis. Enriched Response Elements within the Same Groups of Genes (P-value < 10e-3) Are Indicated as Underlined and Bold According to Athena Visualization Program [71].
| Response elements and conditions under which the elements induce genes | DREB1 | ABRE2 | AHBP3 | GBOX4 | GTBOX5 | LREM6 | CCAF7 | HSF8 | CGCG9 | SALT10 | DOFF11 |
| Cold | ABA | ABA | ABA/Light | Light | Light | Circadian | Heat | Calcium | Salt | Carbon | |
| Target genes, AGI Code, description | |||||||||||
| At1g56600, Galactinol synthetase.C/L | 2 | 7 | 4 | 7 | 6 | 2 | 2 | 0 | 1 | 0 | 1 |
| At1g09350, Galactinol synthase. C/L, C/D | 1 | 3 | 1 | 5 | 2 | 1 | 0 | 0 | 0 | 0 | 1 |
| At3g50970, XERO2, C/L, C/D | 3 | 0 | 5 | 0 | 1 | 3 | 0 | 0 | 0 | 0 | 4 |
| At5g52310, RD29A, C/L, C/D | 4 | 1 | 2 | 3 | 4 | 0 | 0 | 0 | 2 | 1 | 3 |
| At1g20450, ERD10, C/L, C/D | 3 | 2 | 3 | 0 | 3 | 2 | 0 | 1 | 1 | 1 | 3 |
| At5g15960, KIN1, C/L | 1 | 4 | 0 | 4 | 5 | 2 | 0 | 1 | 0 | 0 | 1 |
| At5g66400, RAB18, C/L | 1 | 3 | 4 | 2 | 5 | 0 | 0 | 0 | 2 | 1 | 2 |
| At1g20340, PC, C/L | 1 | 2 | 1 | 5 | 5 | 4 | 0 | 1 | 2 | 3 | 4 |
| At4g11600, GPX, C/L | 1 | 3 | 1 | 8 | 6 | 2 | 1 | 0 | 0 | 1 | 1 |
| At1g77120, ADH, C/L | 0 | 3 | 2 | 3 | 6 | 1 | 1 | 1 | 0 | 0 | 4 |
| At3g08940, LHCB4.2, C/L | 0 | 2 | 2 | 3 | 2 | 3 | 0 | 0 | 0 | 1 | 1 |
| At3g27690, LHCB2.4, C/L | 0 | 1 | 6 | 6 | 1 | 2 | 3 | 1 | 0 | 0 | 1 |
| At2g05070, LHCB2.2, C/L | 0 | 2 | 3 | 3 | 2 | 1 | 1 | 0 | 0 | 1 | 2 |
| At1g29930, LCHB1.3, C/L | 0 | 3 | 1 | 5 | 3 | 7 | 4 | 0 | 0 | 0 | 1 |
| At5g67030, ZEP, C/L | 0 | 3 | 1 | 6 | 3 | 0 | 4 | 0 | 0 | 0 | 1 |
| At5g13930, Chalcone synthase. C/L | 0 | 4 | 1 | 3 | 1 | 3 | 0 | 1 | 0 | 0 | 2 |
| Transcription factor genes | |||||||||||
| At4g25490, DREB1B, C/L, C/D | 0 | 3 | 2 | 5 | 5 | 1 | 0 | 0 | 0 | 0 | 2 |
| At5g05410, DREB2A, C/L, C/D | 0 | 1 | 3 | 2 | 3 | 5 | 1 | 2 | 0 | 0 | 1 |
| At2g46830, CCA1, C/L, C/D | 0 | 3 | 3 | 2 | 4 | 1 | 0 | 1 | 2 | 0 | 3 |
| At1g49720, ABF1, C/L, C/D | 0 | 0 | 0 | 0 | 2 | 2 | 1 | 2 | 0 | 0 | 5 |
| At1g13260, RAV113, C/D, C/L | 0 | 1 | 3 | 0 | 7 | 1 | 0 | 2 | 0 | 0 | 2 |
| At1g51700, ADOF1, C/L | 0 | 0 | 0 | 0 | 9 | 1 | 3 | 1 | 0 | 1 | 2 |
| At4g34590, ATB2-GBF6, C/L | 0 | 0 | 11 | 0 | 6 | 2 | 5 | 0 | 0 | 0 | 4 |
| At5g63790, ANAC10212, C/L | 0 | 6 | 1 | 10 | 1 | 0 | 0 | 0 | 0 | 0 | 2 |
| At5g08790, ATAF212, C/L | 1 | 1 | 3 | 6 | 3 | 2 | 1 | 0 | 0 | 0 | 3 |
| At2g42280, MYC 14 D | 0 | 2 | 2 | 0 | 5 | 3 | 1 | 0 | 0 | 0 | 2 |
| Miscellaneous, Dark induced genes | |||||||||||
| At3g12580, HSP70, C/D | 1 | 0 | 3 | 0 | 6 | 1 | 2 | 5 | 1 | 0 | 2 |
| At2g32950, COP1 regulatory protein, D | 1 | 0 | 3 | 3 | 5 | 0 | 0 | 1 | 2 | 0 | 1 |
| At4g02440, F-box protein, ZGT, D | 0 | 0 | 0 | 1 | 3 | 0 | 0 | 0 | 2 | 0 | 2 |
| Control set of random genes, no changed expression in C/L, C/D or D condition * | |||||||||||
| At2g37460, Root nodulin MtN21 | 0 | 0 | 0 | 0 | 4 | 0 | 1 | 0 | 0 | 0 | 0 |
| At4g12550, Seed lipid transfer protein LTP | 0 | 0 | 3 | 0 | 6 | 0 | 1 | 1 | 0 | 0 | 0 |
| At3g56020, 60S ribosomal protein L41 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 3 | 0 | 1 |
| At4g31700, 40S ribosomal protein RPS6 | 0 | 0 | 5 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 1 |
| At3g47600, MYB94 | 0 | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 1 |
| At1g73460, protein kinase | 0 | 0 | 0 | 0 | 1 | 0 | 2 | 1 | 2 | 0 | 1 |
Footnotes 1–14: References for response elements found in Arabidopsis thaliana.1) [13]; [72] 2) [12] 3) [73]; [74] 4) [75]; [76] 5) [77]; [78] 6) [79]. 7) [80]; [81] 8) [82]; [83] 9) [84] 10) [85]; [86] 11) [87] 12) [88] 13) [89] 14) [90]
* Altogether, the promoter regions of 1000 genes in the Control group were tested with similar results.