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SHR Neuro Cancer Cardio Lipid Metab Microb
Das, SK; Pathak, RR; Choudhury, D; Raghuram, N.
Genomewide computational analysis of nitrate response elements in rice and Arabidopsis.
Mol Genet Genomics. 2007; 278(5):519-525
Doi: 10.1007/s00438-007-0268-3
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- Leading authors Med Uni Graz
- Das Suman Kumar
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- Abstract:
- Nitrate response element (NRE) was originally reported to be comprised of an Ag/cTCA core sequence motif preceded by a 7-bp AT rich region, based on promoter deletion analyses in nitrate and nitrite reductases from Arabidopsis thaliana and birch. In view of hundreds of new nitrate responsive genes discovered recently, we sought to computationally verify whether the above motif indeed qualifies to be the cis-acting NRE for all the responsive genes. We searched for the specific occurrence of at least two copies of the above motif in and around the nitrate responsive genes and elsewhere in the Arabidopsis and rice (Oryza sativa) genomes, with respect to their positional, orientational and strand-specific bias. This is the first comprehensive analysis of NREs for 625 nitrate responsive genes of Arabidopsis and their rice homologs, representing dicots and monocots, respectively. We report that the above motifs are present almost randomly throughout these genomes and do not reveal any specificity or bias towards nitrate responsive genes. This also seems to be true for smaller subsets of nitrate responsive genes in Arabidopsis, such as the 21 early responsive genes, 261 and 90 genes for root-specific and shoot-specific response, respectively, and 25 housekeeping genes. This necessitates a fresh search for candidate sequences that qualify to be NREs in these and other plants.
- Find related publications in this database (using NLM MeSH Indexing)
- Arabidopsis - genetics
- Computational Biology - methods
- Gene Expression Regulation, Plant - methods
- Genes, Plant - methods
- Genetic Techniques - methods
- Genome, Plant - methods
- Models, Biological - methods
- Nitrates - chemistry
- Nitrite Reductases - metabolism
- Oryza sativa - genetics
- Promoter Regions (Genetics) - genetics
- Reverse Transcriptase Polymerase Chain Reaction - genetics
- Signal Transduction - genetics
- Species Specificity - genetics
- Transcription, Genetic - genetics
- Find related publications in this database (Keywords)
- motifs
- nitrate
- promoters
- response elements
- signaling
- transcriptional regulation