Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

Abstract

Significance We use molecular dynamics to simulate reversible binding of proteins to DNA and uncover an unexpected force driving DNA compaction and protein aggregation. In the absence of any explicit interactions between proteins, or between templates, we find proteins aggregate spontaneously to locally organize the genome. The simulations reproduce the structures seen experimentally when small bivalent proteins assemble into rows (like bacterial H-NS protein), larger proteins with eight binding sites into irregular strings (like octameric nucleosomal cores in chromatin fibers), and still-larger complexes representing RNA polymerase II and a transcription factor (NFκB) into clusters surrounded by loops (like transcription factories). We suggest clustering is driven by an entropic bridging-induced attraction that minimizes bending and looping penalties in the template.