Understanding the mechanism of dual bromodomain of TAF1 in DNA interaction and its role in epigenetic gene regulation

Chyne, Phibarisha (2023) Understanding the mechanism of dual bromodomain of TAF1 in DNA interaction and its role in epigenetic gene regulation. Masters thesis, Indian Institute of Science Education and Research Kolkata.

Text (MS dissertation of Phibarisha Chyne (18M102)) Thesis_18MS102.pdf - Submitted Version Restricted to Repository staff only Download (2MB)

Abstract

The bromodomains on TAF1 are known to play an important role in recognizing acetylated marks and thereby docking the protein on active gene regions on which these marks are abundantly present. Along with TBP, TAF1 recruits the pre-initiation complex as a part of TFIID on TATA-box promoters by forming the docking site for others proteins. TAF1 contains two bromodomains present in tandem whose independent roles still remain unclear. Here, we report the significant differences in the two evolutionarily conserved domains that allow for differential recognition to nucleic acids to probe and propose a possible bivalent mechanism through which simultaneous recognition of acetylation marks and nucleic acid can take place through the tandem bromodomains at the active gene regions. We report a novel nucleic acid recognition by the bromodomains of a non-BET protein TAF1. Preliminary analysis of the two bromodomains reveal a stark differential distribution of electrostatic surface potentials on the two proteins and varying pI values for each of them. Using theoretical approaches of molecular docking and simulations we have established the feasibility of an interaction between the first bromodomain, BD1 on the TAF1 protein and dsDNA using the 147bp Widom 601 DNA sequence as a model. EMSA titrations of the wildtype TAF1 tandem bromodomains in several conditions have revealed the validity of binding, further mutants on the alpha helices of the tandem bromodomains reveal the possible binding site for nucleic acid. The results elucidate that the bivalent mechanism of recognising acetylation marks and nucleic acids is promising in the TAF1 tandem bromodomains protein.

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