Genome-wide expression analysis regulated by internal nitrate in Arabidopsis thaliana

The effects of internal nitrate level on transcriptome in Arabidopsis thaliana were analyzed. To manipulate internal nitrate levels independently of internal organic nitrogen, wild-type accession Col and a nitrate reductase (NR)-null mutant were used. Col and the NR-null mutant were grown for 7 days using 2.5 mM ammonium as the sole nitrogen source. The plants were treated with 10 mM nitrate and 2.5 mM ammonium for the first 24 hours so that they would accumulate nitrate. The plants were then transferred to nitrogen-free medium and grown for 5 days. At the time, nitrate concentrations in the shoots of NR-null mutant were significantly larger than those of Col, whilst, in the roots, no significant difference in nitrate concentration was detected between Col and the mutant. Using their shoots and roots, RNA sequencing was performed.