BPS2026 - The occupancy of transcription factor Cbf1/Pho4 at nucleosome entry-exit region

Transcription factors (TFs) function by binding specific DNA sequences in gene promoters/enhancers to initiate transcription. TF binding sites are frequently found within the nucleosome near the DNA entry-exit region. TFs can be roughly divided into two groups: canonical transcription factor (cTF or TF) and pioneer transcription factor (PF). Canonical TFs typically function in regions of open chromatin, where DNA is already accessible, and help recruit the transcriptional machinery to activate or repress gene expression. In contrast, PFs can recognize and bind their target DNA motifs even within condensed, nucleosome-bound chromatin. Why PFs are not inhibited by nucleosomes is less understood. Our recent single-molecule TIRF experiments found that Cbf1, a budding yeast PF, can enhance binding affinity to nucleosomes by slowed dissociation rate from nucleosomes relative to DNA. We also found the interaction between Cbf1’s helix-loop-helix region (HLH) and histone h3 tail is the key factor to its slow dissociation rate. My first project is to investigate the Cbf1-h3 tail interaction dynamics by single-molecule TIRF method. The TF’s DNA binding site position within the nucleosome entry-exit region significantly influences TF occupancy but how is less quantitatively understood. My second work is to probe the targeting and occupancy of Cbf1 at different positions within the nucleosome entry-exit region.