Remodeling Chromatin Induces Z-DNA Conformation Detected through Fourier Transform Infrared Spectroscopy

Anal Chem. 2020 Nov 3;92(21):14452-14458. doi: 10.1021/acs.analchem.0c02432. Epub 2020 Oct 21.

Abstract

The SWI/SNF complex is a highly conserved chromatin remodeling complex and can hydrolyze ATP by its catalytic subunit BRG1 or BRM to reconstruct the chromatin. To investigate whether this ATP-dependent chromatin remodeling could affect the DNA conformation, we therefore regulated (knocked down or overexpressed) BRG1/BRM in the cells and applied Fourier transform infrared (FTIR) spectroscopy to probe DNA conformational changes. As a result, we found that BRG1/BRM was indeed associated with the DNA conformational changes, in which knockdown of BRG1/BRM reduced Z-DNA conformation, while overexpression of BRG1/BRM enhanced Z-DNA conformation. This Z-DNA conformational transformation was also verified using the Z-DNA-binding proteins. Therefore, this work has provided a direct analytical tool to probe Z-DNA transformation upon ATP-dependent chromatin remodeling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / metabolism
  • Cell Line, Tumor
  • Chromatin Assembly and Disassembly*
  • DNA Helicases / deficiency
  • DNA Helicases / genetics
  • DNA, Z-Form / chemistry*
  • DNA, Z-Form / metabolism
  • Gene Knockdown Techniques
  • Humans
  • Nuclear Proteins / deficiency
  • Nuclear Proteins / genetics
  • Nucleic Acid Conformation*
  • Spectroscopy, Fourier Transform Infrared*
  • Transcription Factors / deficiency
  • Transcription Factors / genetics

Substances

  • DNA, Z-Form
  • Nuclear Proteins
  • Transcription Factors
  • Adenosine Triphosphate
  • SMARCA4 protein, human
  • DNA Helicases