A widely applicable and cost-effective method for specific RNA–protein complex isolation

• Published in: Scientific reports Vol. 13; no. 1; pp. 6898 - 19
• Main Authors: Balzarini, Sam, Van Ende, Roosje, Voet, Arnout, Geuten, Koen
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 27-04-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/45/500; 631/45/612/1230; Cost-Benefit Analysis; Efficiency; Humanities and Social Sciences; Methods; multidisciplinary; Proteins; Ribonucleoproteins - metabolism; RNA - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Science; Science (multidisciplinary); Silica
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-34157-0

Although methodological advances have been made over the past years, a widely applicable, easily scalable and cost-effective procedure that can be routinely used to isolate specific ribonucleoprotein complexes (RNPs) remains elusive. We describe the “Silica-based Acidic Phase Separation (SAPS)-capture” workflow. This versatile method combines previously described techniques in a cost-effective, optimal and widely applicable protocol. The specific RNP isolation procedure is performed on a pre-purified RNP sample instead of cell lysate. This combination of protocols results in an increased RNP/bead ratio and by consequence a reduced experimental cost. To validate the method, the 18S rRNP of
S. cerevisiae
was captured and to illustrate its applicability we isolated the complete repertoire of RNPs in
A. thaliana
. The procedure we describe can provide the community with a powerful tool to advance the study of the ribonome of a specific RNA molecule in any organism or tissue type.