Research

Profiling genome specificity

To regulate gene expression, transcription factors (TFs) must bind at specific gene regulation regions. But genomes are vast, and the DNA motifs bound by TFs are short. What makes the TF-target process so specific and rapid? We examine this question by spatially resolved profiling of TF bindings across the human, mouse and yeast genomes, live-cell single-molecule tracking of TFs dynamics, and analysis of TF binding in cell-free systems.

Decoding TF specificity

The function of proteins is often attributed to their structure. Outside of their DNA binding domain (DBD), TFs are characterized by intrinsically disordered regions (IDRs) that lack stable structures. Sequence-function relations in IDRs differ from these of structured domains, making them difficult to study. Based on our recent findings, we hypothesize that IDRs hold the key for specificity by directing TFs across genomes. To establish this new paradigm, we quantify the role of IDRs across TFs, compare its conservation across species and define the molecular and sequence grammar through which IDR can guide the TF-target search.

Decoding DNA specificity

What DNA features, beyond the short DBD-bound motifs, are recognized by TFs? And which are recognized by the TF IDRs? Based on our recent findings, we hypothesize that DNA conformation dynamics hold the key for genomic specificity, by exposing transient helical structures compatible with IDR chemistry. We investigate the DNA-IDR targeting rules by combining massive parallel binding assays inside cells, mutations designed to modulate DNA sequence of conformation, and biophysical binding assays in cell-free systems.