Multiple RNA- and DNA- binding proteins exhibit direct transfer of polynucleotides with implications for target- site search

We previously demonstrated that the polycomb repressive complex 2 chromatin-modifying enzyme can directly transfer between RNA and DNA without a free-enzyme intermedi-ate state. Simulations suggested that such a direct transfer mechanism may be generally necessary for RNA to recruit proteins to chromatin, but the prevalence of direct transfer capability is unknown. Herein, we used fluorescence polarization assays and observed direct transfer for several well-characterized nucleic acid-binding proteins: three -prime repair exo-nuclease 1, heterogeneous nuclear ribonucleoprotein U, Fem- 3-binding factor 2, and MS2 bacteriophage coat protein. For TREX1, the direct transfer mechanism was additionally observed in single-molecule assays, and the data suggest that direct transfer occurs through an unstable ternary intermediate with partially associated polynucleotides. Generally, direct transfer could allow many DNA-and RNA-binding proteins to conduct a one-dimensional search for their target sites. Furthermore, proteins that bind both RNA and DNA might be capable of readily translocating between those ligands.SignificanceClassically, the lifetime of a protein-ligand complex is presumed to be an intrinsic property, unaffected by competitor molecules in free solution. By contrast, a few oligomeric nucleic acid-binding proteins have been observed to exchange competing ligands in their binding sites, and consequently their lifetimes decrease with competitor concentration. Our findings suggest that this direct transfer capability may be a more general property of nucleic acid- binding proteins. Thus, many DNA-and RNA-binding proteins could reduce the dimensionality of their search for their target sites by direct transfer to nucleosome DNA, instead of relying entirely on three-dimensional diffusion. Furthermore, direct transfer from nascent RNA to DNA may explain why so many DNA-binding proteins also bind RNA.

Automated summary

We have demonstrated that the polycomb repressive complex 2 chromatin-modifying enzyme can directly transfer between RNA and DNA without a free-enzyme intermediate state. This direct transfer mechanism has been observed in several well-characterized nucleic acid-binding proteins, indicating its prevalence. The ability of proteins to conduct a one-dimensional search for their target sites through direct transfer may have important implications for understanding gene regulation and protein-ligand interactions.