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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].

From: Light has a specific role in modulating Arabidopsis gene expression at low temperature

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
  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]
  2. * Altogether, the promoter regions of 1000 genes in the Control group were tested with similar results.