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.
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Acknowledgments
This work was supported in part by research grants from DST (No. SP/SO/BB-27/2002) and CSIR (No. 60/(0056)/02/EMR-II) awarded to N. Raghuram. The authors wish to thank Chiradeep Sarkar, Priyanka Sharma, Dr. B. Vani and Dr. Nimisha Sharma and for their suggestions and help at various stages of this work.
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Communicated by Y. Van de Peer .
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Figure S1. Strand wise distribution of the Ag/cTCA motif in the up- regulated nitrate responsive genes of Arabidopsis (TIF 6.76 mb)
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Figure S2. Strand wise distribution of the Ag/cTCA motif in the down- regulated nitrate responsive genes of Arabidopsis (TIF 6.73 mb)
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Figure S3. Strand wise distribution of the Ag/cTCA motif in different subsets of nitrate responsive genes of Arabidopsis (TIF 421 kb)
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Figure S4. Distribution of the spacing between adjacent Ag/cTCA motif with respect to DNA helicity in the upstream regions of nitrate responsive genes of Arabidopsis (TIF 6.29 mb)
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Figure S5. Distribution of the spacing between adjacent Ag/cTCA motif with respect to DNA helicity in the downstream regions of nitrate responsive genes of Arabidopsis (TIF 5.79 mb)
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Figure S6. Distribution of the spacing between adjacent Ag/cTCA motif with respect to DNA helicity within the coding regions of nitrate responsive genes of Arabidopsis (TIF 6.29 mb)
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Das, S.K., Pathak, R.R., Choudhury, D. et al. Genomewide computational analysis of nitrate response elements in rice and Arabidopsis . Mol Genet Genomics 278, 519–525 (2007). https://doi.org/10.1007/s00438-007-0268-3
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DOI: https://doi.org/10.1007/s00438-007-0268-3