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

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

AGI number	Gene Annotation	Responsiveness to nitrate	Methylation status^a
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

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].

ISSN: 1471-2164