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Pak. J. Bot., 45(SI): 309-319, 2013.

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IN SILICO PREDICTION OF REGULATORY ELEMENTS AND CORRESPONDING PROTEIN-DNA INTERACTIONS IN PLANT PROMOTERS

MADIHA TANVEER, HINA-UR-RAZAQ QURESHI, M. QAISER FATMI AND TAYYABA YASMIN*

Abstract: The importance of cis or trans acting regulatory elements in gene regulation is quite obvious. Exploring these elements in vivo demands extensive experimentation and is time intensive. In silico methods of predicting these elements have been developed in this regard. In present study around 300 promoters belonging to monocots, dicots and algae were analysed through Consite tool for prediction of regulatory elements. Many putative regulatory elements of diverse functions were found in these promoters. In monocots, TATA-binding proteins (TBP), in dicots, hunchback and in Algae, aryl hydrocarbon receptor nuclear translocator (ARNT) were abundantly represented with 55, 33 and 86% respectively. It was observed that all three plant groups exhibited different families of transcription factors like basic helix-loop-helix (bHLH), basic helix-loop-helix leucine zipper (bHLH-ZIP), Forkhead, RUNT, HOMEO-ZIP, zinc finger (ZN-FINGER), REL, Nuclear receptor, MADS, bZIP and TATA-box. Moreover, selected transcription factors were explored through HADDOCK Webserver to predict possible interactions between their corresponding regulatory elements. It was observed that hydrogen bonds were mostly involved in these interactions. In addition, Lysine and Arginine were mainly found to be associated in establishing these interactions with thymine base.

Department of Bioscience, COMSATS Institute of Information Technology (CIIT) Islamabad, Campus, Pakistan.

*Corresponding author e-mail: tayyaba_yasmin@comsats.edu.pk