19th-banner-rev.gif

Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

In Silico Analysis of Structural Properties of Fungal DNA Sequences and Promoter Prediction

Promoters play a central role in transcription initiation and gene regulation, so it is necessary for these DNA regions to be differentiated from non-promoter sequences. Sequence motif based computational methods have not been able to identify these regions with high degree of sensitivity and precision. On the other hand several experimental and computational studies have shown that promoter sequences possess some special properties, which are common across all organisms. In the current in silico study, we examined genomic regions upstream of genes of S. cerevisiae with respect to their transcription start sites as well as the upstream regions in all 7 yeast species with respect to their translation start sites, to see the differences in their predicted structural features (stability, bendability and nucleosome positioning preference, curvature, 2, 3). The core promoter regions show different structural properties like lower stability, lower bendability and slightly higher curvature compared to other neighbouring regions (1). Moreover we also observed that TATA-containing promoters are less stable, more flexible and more curved compared to TATA-less promoters, but both have similar nucleosome positioning preferences. The variability of structural properties of TATA-less and TATA-containing promoters may be due to differences in their role in regulation of gene expression. Detailed analysis of these promoters, comparison with results for prokaryotic promoters (4, 5) as well as quantitative prediction ability of our in-house software ‘PromPredict’ will be presented.

References

  1. A. Kanhere and M. Bansal, Nucleic Acids Res. 33, 3165-3175 (2005).
  2. F. Cui and V. B. Zhurkin, J Biomol Struct Dyn 27, 821-841 (2010).
  3. D. Wang, N. B. Ulyanov, and V. B. Zhurkin, J Biomol Struct Dyn 27, 843-859 (2010).
  4. V. Rangannan and M. Bansal, Mol. BioSyst. 5, 1758-1769 (2009).
  5. V. Rangannan and M. Bansal, Bioinformatics 26, 3043-3050(2010).

Manju Bansal
Venkata Rajesh Yella

Molecular Biophysics Unit
Indian Institute of Science
Bangalore 560012, India

Ph: +91-80-22932534
mb@mbu.iisc.ernet.in