2 PhD’s to study transcription factor binding at the single-molecule level

Precise regulation of transcription is essential to ensure that the correct genes are expressed in the correct tissue at the correct time. At the basis of gene regulation are gene-specific transcription factors (TFs), which are essential to activate or repress transcription of their target genes in specific tissues. Previous work from our and other labs (Pomp, Mol Cell, 2024) have shown that many TFs bind to DNA cooperatively, but how this cooperativity is established is largely unclear. In the first project (Tineke Lenstra group, NKI), we aim to uncover how transcription factor binding dynamics and cooperativity are regulated by nucleosomes, self-interactions, and DNA shape, and how these mechanisms regulate single-cell transcription dynamics. In the second project (John van Noort group, Leiden University), we will design and build custom chromatin fibers to resolve how these are folded into higher-order structures and how chromatin structure affects transcription factor binding. The projects are tightly linked, and it is anticipated that both PhD’s work together closely.

In collaboration with LUMICKS, manufacturer of C-trap instrumentation, we will setup a novel single-molecule imaging system to measure and perturb the DNA binding kinetics of transcription factors ex vivo and develop a novel assay to map the position of nucleosomes along single chromatin fibers. Moreover, we will exploit the unique opportunity to integrate these ex vivo results with simultaneous DNA binding and transcription measurements at a single locus in living yeast cells using our novel tracking technology (Pomp, Mol Cell, 2024). This powerful ex vivo-in vivo combination will allow us to gain quantitative insight into the different mechanisms of transcription factors cooperativity in gene regulation at single molecule resolution.