title: Genome-wide analysis of overlapping genes regulated by iron deficiency and phosphate starvation reveals new interactions in Arabidopsis roots.
abstract: BACKGROUND
  Iron (Fe) and phosphorus (P) are essential mineral nutrients in plants. Knowledge regarding global changes in the abundance of Fe-responsive genes under Pi deficiency as well as the processes these genes are involved in remains largely unavailable at the genome level. In the current study, we comparatively analyzed RNA sequencing data sets relative to Fe deficiency (NCBI: SRP044814) and Pi starvation (NCBI: SRA050356.1).
  
  
  RESULTS
  Analysis showed a total of 579 overlapping genes that are responsible for both Fe deficiency and Pi starvation in Arabidopsis roots. A subset of 137 genes had greater than twofold changes in transcript abundant as a result of the treatments. Gene ontology (GO) analysis showed that the stress-related processes 'response to salt stress', 'response to oxidative stress', and 'response to zinc ion' were enriched in the 579 genes, while Fe response-related processes, including 'cellular response to nitric oxide', 'cellular response to iron ion', and 'cellular iron ion homeostasis', were also enriched in the subset of 137 genes. Co-expression analysis of the 579 genes using the MACCU toolbox yielded a network consisting of 292 nodes (genes). Further analysis revealed that a subset of 90 genes were up-regulated under Fe shortage, but down-regulated under Pi starvation. GO analysis in this group of genes revealed an increased cellular response to iron ion/nitric oxide/ethylene stimuli. Promoter analysis was performed in 35 of the 90 genes with a 1.5-fold or greater change in abundance, showing that 12 genes contained the PHOSPHATE STARVATION RESPONSE1-binding GNATATNC cis-element within their promoter regions. Quantitative real-time PCR showed that the decreased abundance of Fe acquisition genes under Pi deficiency exclusively relied on Fe concentration in Pi-deficient media.
  
  
  CONCLUSIONS
  Comprehensive analysis of the overlapping genes derived from Fe deficiency and Pi starvation provides more information to understand the link between Pi and Fe homeostasis. Gene clustering and root-specific co-expression analysis revealed several potentially important genes which likely function as putative novel players in response to Fe and Pi deficiency or in cross-talk between Fe-deficient responses and Pi-deficient signaling.
authors.affiliation: Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, People's Republic of China. wfli@njfu.edu.cn.|State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China. wfli@njfu.edu.cn.
authors.forename: Wenfeng
authors.initials: W
authors.lastname: Li
authors.affiliation: State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China. plan@issas.ac.cn.
authors.forename: Ping
authors.initials: P
authors.lastname: Lan
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D016000:Cluster Analysis; D015536:Down-Regulation / Q000235:genetics; D004843:Epistasis, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D005807:Genes, Overlapping; D017343:Genes, Plant; D055106:Genome-Wide Association Study; D000090463:Iron Deficiencies; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs / Q000235:genetics; D010710:Phosphates / Q000172:deficiency*; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D010710:Phosphates; D012333:RNA, Messenger