Shantanu Chowdhury is interested in exploring the functional relevance of DNA secondary structures like G quadruplexes at a genome-wide and molecular level.
His major interests are:
Deciphering the role of G quadruplexes in gene regulation in general and the regulation of c-myc in particular
Understanding the mechanism of action of metastasis suppressor NM23-H2
His laboratory has shown the prevalence and conservation of potential G-quadruplex forming sequences in regulatory regions in prokaryotes and eukaryotes using genome informatics. Whole genome expression studies using ligand-induced perturbation of the intracellular G4 DNA motif formation in human cell lines substantiated the in-silico results. His work shows that a transcription factor NM23-H2 is involved in transcriptional activation of c-myc through quaduplex formation.
- Metastases suppressor NM23-H2 interaction with G-quadruplex DNA within c-MYC promoter nuclease hypersensitive element induces c-MYC expression. Thakur, R. K., Kumar, P., Halder, K., Verma, A., Kar, A., Parent, J. L., Basundra, R., Kumar, A., and Chowdhury, S. Nucleic Acids Res. 2009. 37, 172-183.
- Evidence of genome-wide G4 DNA-mediated gene expression in human cancer cells. Verma, A., Yadav, V. K., Basundra, R., Kumar, A., and Chowdhury, S. Nucleic Acids Res. 2009. 37, 4194-4204.
- Genome-wide computational and expression analyses reveal G-quadruplex DNA motifs as conserved cis-regulatory elements in human and related species. Verma, A., Halder, K., Halder, R., Yadav, V. K., Rawal, P., Thakur, R. K., Mohd, F., Sharma, A., and Chowdhury, S. J.Med.Chem. 2008. 51, 5641-5649.
- Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation. Rawal, P., Kummarasetti, V. B., Ravindran, J., Kumar, N., Halder, K., Sharma, R., Mukerji, M., Das, S. K., and Chowdhury, S. Genome Res. 2006. 16, 644-655.
- Kinetic resolution of bimolecular hybridization versus intramolecular folding in nucleic acids by surface plasmon resonance: application to G-quadruplex/duplex competition in human c-myc promoter. Halder, K. and Chowdhury, S. Nucleic Acids Res. 2005. 33, 4466-4474.