Table 2. TF Genes That Are Directly Targeted and Positively Regulated by RIN Found by ChIP-chip and Transcriptome Analysis in This Study.
| Microarray Gene Expression |
ChIP-chipb | ||||
|---|---|---|---|---|---|
| ITAG2 Gene ID | Description | FCWTc | FCrind | ECSe | Peak Score (Log2) |
| Solyc05g012020 | MADS box TF (RIN) | 847.2 | 70f | 12.1 | 1.40 |
| Solyc07g052960 | GRAS family TF (SCL32-like) | 683.5 | 6.8 | 100.6 | 1.43, 1.57 |
| Solyc10g079050a | BHLH TF (bHLH130 homolog) | 23.8 | 1.3 | 17.7 | 1.84 |
| Solyc05g007770a | NAC domain TF (NAP homolog) | 17.8 | 2.5 | 7.2 | 1.11 |
| Solyc08g063040a | Zinc-finger protein (IDD2 homolog) | 17.4 | 1.7 | 10.4 | 1.75, 1.65 |
| Solyc03g044300a | AP2-like ethylene-responsive TF (AP2a) | 15.8 | 1.7 | 9.0 | 1.96, 1.76 |
| Solyc01g100460a | BZIP TF (ABZ1) | 12.1 | 3.0 | 4.0 | 1.31 |
| Solyc10g006880 | NAC domain protein (NOR) | 9.4 | 4.6 | 2.1 | 1.97 |
| Solyc02g077920 | Squamosa promoter binding-like protein (C) | 4.8 | 1.7 | 2.8 | 1.87 |
| Solyc07g054450a | TF (fragment) ULTRAPETALA1 (ULT1 homolog) | 4.1 | 1.9 | 2.2 | 1.53, 1.57 |
| Solyc01g008910a | Scarecrow TF family protein (SCL3 homolog) | 4.0 | 1.1 | 3.7 | 1.50 |
| Solyc02g085630g | Homeobox-Leucine-zipper-like protein (HB40 homolog) | 2.9 | 0.3 | 9.1 | 1.52 |
| Solyc07g041190a |
Alfin-like 5 PHD finger family protein (AL5 homolog) | 2.5 | 1.2 | 2.1 | 1.44 |
| Solyc12g099340a | Calmodulin binding transcription activator 5 (SR3L) | 2.3 | 0.9 | 2.4 | 1.28 |
Direct RIN target genes newly identified.
All RIN binding sites presented here were located in the gene promoters. When there were two sites in a gene regulatory and transcribed region, both site values are listed.
FC value of a gene in the wild-type tomato fruits at the ripening (P) stage relative to that at the preripening (G) stage.
FC value of a gene in the rin mutant tomato fruits at the same age as the wild-type P stage relative to that at the same age as the wild-type G stage.
ECS is the ratio of FCWT to FCrin, representing the dependency of gene expression on RIN.
The apparent RIN expression in the rin mutant due to the expression of mutated rin gene.
Solyc02g085630 was eliminated later from the subset because qRT-PCR did not reproduce the ripening-induced expression obtained by the microarray analysis.