Dual tagging as an approach to isolate endogenous chromatin remodeling complexes from Saccharomyces cerevisiae

•Development of a dual tagging approach based on a Protein A and a Twin-Strep tag•Isolation of endogenous RSC complexes under mild purification conditions from yeast•Enrichment of intact RSC complexes relative to individual proteins and subcomplexes•Isolated RSC complexes are functionally active and structurally well defined•Conformational rearrangement of RSC upon binding of an acetylated histone H3 peptide

Affinity isolation has been an essential technique for molecular studies of cellular assemblies, such as the switch/sucrose non-fermentable (SWI/SNF) family of ATP-dependent chromatin remodeling complexes. However, even biochemically pure isolates can contain heterogeneous mixtures of complexes and their components. In particular, purification strategies that rely on affinity tags fused to only one component of a complex may be susceptible to this phenomenon. This study demonstrates that fusing purification tags to two different proteins enables the isolation of intact complexes of remodels the structure of chromatin (RSC). A Protein A tag was fused to one of the RSC proteins and a Twin-Strep tag to another protein of the complex. By mass spectrometry, we demonstrate the enrichment of the RSC complexes. The complexes had an apparent Svedberg value of about 20S, as shown by glycerol gradient ultracentrifugation. Additionally, purified complexes were demonstrated to be functional. Electron microscopy and single-particle analyses revealed a conformational rearrangement of RSC upon interaction with acetylated histone H3 peptides. This purification method is useful to purify functionally active, structurally well-defined macromolecular assemblies.