Exploration of DNA binding selectivity, transcriptional regulation, and evolutionary relationships of the Hox protein Ultrabithorax
Matthews, Kathleen S.
Doctor of Philosophy
Hox transcription factors direct differentiation in all tissue layers and many organ systems and therefore have highly specific tissue-dependent functions. The DNA-binding homeodomain of Hox proteins can bind a wide array of nucleotide sequences with similar high affinities, suggesting regions outside the homeodomain must impact DNA interaction. Utilizing a series of deletion mutants, we identified three binding affinity modulation regions outside the homeodomain. DNA binding is inhibited ∼2-fold by the YPWM motif and microexon regions (I1) and ∼40-fold by the large disordered I2 region. High affinity binding is partially restored by the N-terminal 174 residues (R region) in a length-dependent manner. Both I2 and R regions partially overlap the Ubx transcription activation domain, allowing communication between these functional systems. Evolutionary variations in the amino acid sequences of most of these regions potentially differentiate Ubx•DNA interactions.
Biophysics; Biological sciences; DNA binding Hox proteins; Transcriptional regulation; Ultrabithorax