Mapping of Transcription Factor Binding Sites and DNA-Binding Motifs
Date Issued
2008
Date
2008
Author(s)
Liu, Kai-Wei
Abstract
Transcription factors (TFs) play an essential role in gene regulation by activating or inhibiting the expressions of the corresponding genes. The transcription factors carry out their functions by docking at a specific region in the DNA sequence, which is normally referred to as transcription factor binding site (TFBS). Since the complete network of the interactions between TFs and genes is still largely unknown, figuring out the key residues in the DNA binding domain of a TF can provide the biochemists with valuable information for design of biochemical experiments to verify the interactions between the TF and the corresponding genes. Furthermore, with the key residues in the DNA binding domain identified, we can move to establish a mapping between the DNA binding motifs and the TFBS motifs. In the study reported in this thesis, we have proposed a novel approach to achieve the objectives mentioned above. The proposed approach begins with clustering the TFBSs with the same binding type. Then, sequence alignment with a strict criterion is applied to the corresponding DNA binding domains of the TFBSs in the same cluster in order to identify the key residues in the DNA binding domains. For those TFs whose tertiary structure is present in the Protein Data Bank (PDB), we have examined the physiochemical significance of the key residues identified.
Subjects
TFBS
DNA-binding motif
PFM clustering
Type
thesis
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