Characterization of cis-regulatory elements and transcription factor binding: Gel mobility shift assay

Academic Article

Abstract

  • To understand how cardiac gene expression is regulated, the identification and characterization of cfr-regulatory elements and their trans-acting factors by gel mobility shift assay (GMSA) or gel retardation assay are essential and common steps. In addition to providing a general protocol for GMSA, this chapter describes some applications of this assay to characterize cardiac-specific and ubiquitous frarw-acting factors bound to regulatory elements [novel TCTG(G/C) direct repeat and A/T-rich region] of the rat cardiac troponin T promoter. In GMSA, the specificity of the binding of trans-acting factor to labeled DNA probe should be verified by the addition of unlabeled probe in the reaction mixture. The migratory property of DNA-protein complexes formed by protein extracts prepared from different tissues can be compared to determine the tissue specificity of trans-acting factors. GMSA, coupled with specific antibody to DNA-acting factor (antibody supershift assay), is used to identify proteins present in the DNA-protein complex. The gel-shift competition assay with an unlabeled probe containing a slightly different sequence is a powerful technique used to assess the sequence specificity and relative binding affinity of a DNA-protein interaction. GMSA with SDS-PAGE fractionated proteins allows for the determination of the apparent, molecular mass of bound trans-acting factor. © Humana Press Inc.
  • Authors

    Published In

    Digital Object Identifier (doi)

    Author List

  • Lin JJC; Grosskurth SE; Harlan SM; Gustafson-Wagner EA; Wang Q
  • Start Page

  • 183
  • End Page

  • 201
  • Volume

  • 366