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 ExpressionChIP-chipb
ITAG2 Gene IDDescriptionFCWTcFCrindECSePeak Score (Log2)
Solyc05g012020MADS box TF (RIN)847.270f12.11.40
Solyc07g052960GRAS family TF (SCL32-like)683.56.8100.61.43, 1.57
Solyc10g079050aBHLH TF (bHLH130 homolog)23.81.317.71.84
Solyc05g007770aNAC domain TF (NAP homolog)17.82.57.21.11
Solyc08g063040aZinc-finger protein (IDD2 homolog)17.41.710.41.75, 1.65
Solyc03g044300aAP2-like ethylene-responsive TF (AP2a)15.81.79.01.96, 1.76
Solyc01g100460aBZIP TF (ABZ1)12.13.04.01.31
Solyc10g006880NAC domain protein (NOR)9.44.62.11.97
Solyc02g077920Squamosa promoter binding-like protein (C)4.81.72.81.87
Solyc07g054450aTF (fragment) ULTRAPETALA1 (ULT1 homolog)4.11.92.21.53, 1.57
Solyc01g008910aScarecrow TF family protein (SCL3 homolog)4.01.13.71.50
Solyc02g085630gHomeobox-Leucine-zipper-like protein (HB40 homolog)2.90.39.11.52
Solyc07g041190aAlfin-like 5 PHD finger family protein (AL5 homolog)2.51.22.11.44
Solyc12g099340aCalmodulin binding transcription activator 5 (SR3L)2.30.92.41.28
  • a Direct RIN target genes newly identified.

  • b 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.

  • c FC value of a gene in the wild-type tomato fruits at the ripening (P) stage relative to that at the preripening (G) stage.

  • d 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.

  • e ECS is the ratio of FCWT to FCrin, representing the dependency of gene expression on RIN.

  • f The apparent RIN expression in the rin mutant due to the expression of mutated rin gene.

  • g Solyc02g085630 was eliminated later from the subset because qRT-PCR did not reproduce the ripening-induced expression obtained by the microarray analysis.