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This article is part of the supplement: Eighth International Conference on Bioinformatics (InCoB2009): Computational Biology

Open Access Proceedings

Computational identification and experimental validation of PPRE motifs in NHE1 and MnSOD genes of Human

Gireedhar Venkatachalam1, Alan Prem Kumar23, Loo Ser Yue2, Shazib Pervaiz456, Marie Veronique Clement14* and Meena Kishore Sakharkar78*

Author Affiliations

1 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore

2 National University Medical Institutes, Yong Loo Lin School of Medicine, National University of Singapore, Singapore

3 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore

4 NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore

5 Duke-NUS Graduate Medical School, Singapore, Singapore

6 Singapore-MIT Alliance, Singapore

7 Biomedical Engineering Research Centre, Nanyang Technological University, Singapore

8 Advanced Design and Modeling Lab, Nanyang Technological University, Singapore

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BMC Genomics 2009, 10(Suppl 3):S5  doi:10.1186/1471-2164-10-S3-S5

Published: 3 December 2009

Abstract

Background

Activation of PPARs has been reported to inhibit the proliferation of malignant cells from different lineages. They are involved in transcription regulation of genes upon activation by a ligand. The binding of PPARs to the promoter sequence either represses or activates the gene. Hence, PPARs represent promising targets for cancer treatment because of their anti-proliferative and pro-apoptotic activities. Here we computationally identified PPAR binding regions in NHE1 and MnSOD. We further validated the predictions in vitro.

Results

Our results computationally predicted the presence of 2 PPRE motifs in NHE1 and 3 PPRE motifs in MnSOD. We experimentally confirmed the true motifs and their regulation by PPAR.

Conclusion

Our results suggest that both NHE1 and MnSOD have PPRE binding motif in their upstream/promoter region and hence are regulated by PPAR upon ligand binding.