Biochemical assays for analyzing activities of ATP-dependent chromatin remodeling enzymes

J Vis Exp. 2014 Oct 25:(92):e51721. doi: 10.3791/51721.

Abstract

Members of the SNF2 family of ATPases often function as components of multi-subunit chromatin remodeling complexes that regulate nucleosome dynamics and DNA accessibility by catalyzing ATP-dependent nucleosome remodeling. Biochemically dissecting the contributions of individual subunits of such complexes to the multi-step ATP-dependent chromatin remodeling reaction requires the use of assays that monitor the production of reaction products and measure the formation of reaction intermediates. This JOVE protocol describes assays that allow one to measure the biochemical activities of chromatin remodeling complexes or subcomplexes containing various combinations of subunits. Chromatin remodeling is measured using an ATP-dependent nucleosome sliding assay, which monitors the movement of a nucleosome on a DNA molecule using an electrophoretic mobility shift assay (EMSA)-based method. Nucleosome binding activity is measured by monitoring the formation of remodeling complex-bound mononucleosomes using a similar EMSA-based method, and DNA- or nucleosome-dependent ATPase activity is assayed using thin layer chromatography (TLC) to measure the rate of conversion of ATP to ADP and phosphate in the presence of either DNA or nucleosomes. Using these assays, one can examine the functions of subunits of a chromatin remodeling complex by comparing the activities of the complete complex to those lacking one or more subunits. The human INO80 chromatin remodeling complex is used as an example; however, the methods described here can be adapted to the study of other chromatin remodeling complexes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Video-Audio Media

MeSH terms

  • ATPases Associated with Diverse Cellular Activities
  • Adenosine Triphosphatases / chemistry
  • Adenosine Triphosphatases / metabolism*
  • Adenosine Triphosphate / chemistry
  • Adenosine Triphosphate / metabolism
  • Chromatin / chemistry
  • Chromatin / metabolism*
  • DNA / chemistry
  • DNA / metabolism
  • DNA Helicases / chemistry
  • DNA Helicases / metabolism*
  • DNA-Binding Proteins
  • HeLa Cells
  • Humans
  • Nucleosomes / chemistry
  • Nucleosomes / metabolism

Substances

  • Chromatin
  • DNA-Binding Proteins
  • Nucleosomes
  • Adenosine Triphosphate
  • DNA
  • Adenosine Triphosphatases
  • ATPases Associated with Diverse Cellular Activities
  • DNA Helicases
  • INO80 protein, human