Identification of tissue-specific DNA-protein binding sites by means of two-dimensional electrophoretic mobility shift assay display

Anal Biochem. 2007 May 1;364(1):60-6. doi: 10.1016/j.ab.2007.01.040. Epub 2007 Feb 2.

Abstract

We developed a technique of differential electrophoretic mobility shift assay (EMSA) display allowing identification of tissue-specific protein-binding sites within long genomic sequences. Using this approach, we identified 10 cell type-specific protein-binding sites (protein target sites [PTSs]) within a 137-kb human chromosome 19 region. In general, tissue-specific binding of proteins from different nuclear extracts by individual PTSs did not follow the all-or-nothing principle. Most often, PTS-protein complexes were formed in all cases, but they were different for different nuclear extracts used.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites / genetics
  • Cell Nucleus / metabolism
  • Cells, Cultured
  • Chromosome Mapping / methods*
  • DNA-Binding Proteins / chemistry*
  • Data Display*
  • Electrophoresis, Agar Gel
  • Electrophoresis, Gel, Two-Dimensional
  • Electrophoresis, Polyacrylamide Gel
  • Electrophoretic Mobility Shift Assay / instrumentation
  • Electrophoretic Mobility Shift Assay / methods*
  • Gene Library*
  • Genetic Techniques
  • Humans
  • Isoelectric Focusing
  • Nuclear Proteins / genetics
  • Sensitivity and Specificity
  • Tissue Distribution
  • Transcription Factors / chemistry*

Substances

  • DNA-Binding Proteins
  • Nuclear Proteins
  • Transcription Factors