Genome-wide analysis of nutrient-responsive alteration in transcript structures and accumulations in Arabidopsis thaliana

Alteration of transcript structure represents an important step of regulation of gene function. To analyze genome wide response of exon combination patterns under nutrient deficiencies in plants, we performed paired-end RNA sequencing (illumine HiSeq2000) for the roots of Arabidopsis thaliana (Col-0) exposed to deficiencies of 12 different nutrients (N, K, Ca, Mg, P, S, B, Fe, Mn, Zn, Cu, Mo) and un-exposed control plants. Transcripts were assembled and quantified, and the relative abundances of transcript isoforms in each gene were compared among nutrient deficient conditions. We eventually obtained global and comprehensive data of regulatory exon combinations affected by nutritional conditions.