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Table 3 Relationship between the methylation status and nitrate regulation of TCA cycle genes.

From: The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana

AGI number Gene Annotation Responsiveness to nitrate Methylation statusa
At3g47520 MDH (malate dehydrogenase); malate dehydrogenase 3 U
At1g04410 malate dehydrogenase, cytosolic, putative 0 A
At1g53240 malate dehydrogenase (NAD), mitochondrial 0 M
At2g22780 PMDH1 (PEROXISOMAL NAD-MALATE DEHYDROGENASE 1); malate dehydrogenase 0 M
At3g15020 malate dehydrogenase (NAD), mitochondrial, putative 0 U
At5g09660 PMDH2 (PEROXISOMAL NAD-MALATE DEHYDROGENASE 2), PMDH2 (PEROXISOMAL NAD-MALATE DEHYDROGENASE 2); malate dehydrogenase 0 M
At5g56720 malate dehydrogenase, cytosolic, putative 0 M
At5g58330 malate dehydrogenase (NADP), chloroplast, putative 0 M
At5g43330 malate dehydrogenase, cytosolic, putative 0 U
At5g03290 isocitrate dehydrogenase, putative/NAD+ isocitrate dehydrogenase, putative 2 U
At4g35260 IDH1 (ISOCITRATE DEHYDROGENASE 1); isocitrate dehydrogenase (NAD+) 2 U
At1g65930 isocitrate dehydrogenase, putative/NADP+ isocitrate dehydrogenase, putative 1 U
At3g09810 isocitrate dehydrogenase, putative/NAD+ isocitrate dehydrogenase, putative 0 M
At4g35650 isocitrate dehydrogenase, putative/NAD+ isocitrate dehydrogenase, putative 0 U
At5g14590 isocitrate dehydrogenase, putative/NADP+ isocitrate dehydrogenase, putative 0 M
At1g54340 ICDH (ICDH); isocitrate dehydrogenase (NADP+) 0 M
  1. This table provides the AGI number, the gene annotation, regulation by nitrate as determined from four independent experiments (see main text) and the methylation status according to the two methylome datasets used in this work. This table includes all the different malate dehydrogenase and isocitrate dehydrogenase isozyme-coding genes present in the Arabidopsis genome, according to VirtualPlant http://www.virtualplant.org. aMethylation code: U, unmethylated in both datasets; M, methylated in both datasets; A, ambiguous according to Zilberman et al. [25] but unmethylated according to Zhang et al. [24].