DNA Sequence-Dependent Structure Formation in the Cell Nucleus

Objetivo

Only ~1.5% of the human genome encodes proteins; the remaining 98.5%, once dismissed as “junk”, harbors the regulatory blueprint of life. Non-coding DNA controls when and where genes switch on by guiding transcription factor (TF) binding and nucleosome organization, shaping nuclear architecture. Yet how billions of weak, dispersed interactions achieve the high level of specificity required for gene regulation remains a central mystery. Isolated TF binding is far too weak: targeting a single genomic site in the human genome would require >20 kBT of discrimination, while typical TFs reach at most ~10 kBT. This order‑of‑magnitude lack of specificity implies that collective processes underpin mesoscale nuclear structure.

Our work shows that these collective processes are sequence‑guided: TFs can undergo sequence‑dependent prewetting transitions to form TF condensates at specific locations. DNA thus encodes a rugged energy landscape that programs where droplets, loops, and topologically associating domains (TADs) emerge. In collective processes many weak interactions can outcompete a few strong ones, but current approaches fail to capture the vast sequence space of weak binding. We will develop Ising-like models of TF-DNA binding with sub-kBT precision for any sequence, calibrated by competitive binding assays and validated using optical tweezers coupled with MINSTED nanoscopy for near base pair resolution imaging of TFs on stretched DNA. These models will underpin a theory of structure formation via sequence-guided condensation and wetting, tested through optical tweezer-based measurements of prewetting and co-condensation. We will apply this framework to investigate the physical basis of promoter-enhancer communication and TAD-scale genome folding, and evaluate its impact on gene expression levels in cells. This project will establish a physical foundation for sequence-guided genome organization at the mesoscale and its future exploration in development and disease.