Purification and analysis of endogenous human RNA exosome complexes
- Michal Domanski1,2,7,
- Paula Upla1,3,
- William J. Rice4,
- Kelly R. Molloy5,
- Natalia E. Ketaren1,
- David L. Stokes3,
- Torben Heick Jensen2,
- Michael P. Rout1 and
- John LaCava1,6
- 1Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
- 2Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
- 3Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
- 4Simons Electron Microscopy Center at New York Structural Biology Center, New York, New York 10027, USA
- 5Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
- 6Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Corresponding author: jlacava{at}rockefeller.edu
Abstract
As a result of its importance in key RNA metabolic processes, the ribonucleolytic RNA exosome complex has been the focus of intense study for almost two decades. Research on exosome subunit assembly, cofactor and substrate interaction, enzymatic catalysis and structure have largely been conducted using complexes produced in the yeast Saccharomyces cerevisiae or in bacteria. Here, we examine different populations of endogenous exosomes from human embryonic kidney (HEK) 293 cells and test their enzymatic activity and structural integrity. We describe methods to prepare EXOSC10-containing, enzymatically active endogenous human exosomes at suitable yield and purity for in vitro biochemistry and negative stain transmission electron microscopy. This opens the door for assays designed to test the in vitro effects of putative cofactors on human exosome activity and will enable structural studies of preparations from endogenous sources.
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Footnotes
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.057760.116.
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Freely available online through the RNA Open Access option.
- Received May 31, 2016.
- Accepted June 14, 2016.
This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
