{Reference Type}: Journal Article
{Title}: Specific protein-RNA interactions are mostly preserved in biomolecular condensates.
{Author}: de Vries T;Novakovic M;Ni Y;Smok I;Inghelram C;Bikaki M;Sarnowski CP;Han Y;Emmanouilidis L;Padroni G;Leitner A;Allain FH;
{Journal}: Sci Adv
{Volume}: 10
{Issue}: 10
{Year}: 2024 Mar 8
{Factor}: 14.957
{DOI}: 10.1126/sciadv.adm7435
{Abstract}: Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. Our approach offers a procedure to derive structural information of protein-RNA complexes within biomolecular condensates that could be critical for integrative structural modeling of ribonucleoproteins (RNPs) in this form.