Solution AFM studies of human Swi-Snf and its interactions with MMTV DNA and chromatin

Biophys J. 2005 Nov;89(5):3386-98. doi: 10.1529/biophysj.105.065391. Epub 2005 Aug 12.

Abstract

ATP-dependent nucleosome remodeling complexes are crucial for relieving nucleosome repression during transcription, DNA replication, recombination, and repair. Remodeling complexes can carry out a variety of reactions on chromatin substrates but precisely how they do so remains a topic of active inquiry. Here, a novel recognition atomic force microscopy (AFM) approach is used to characterize human Swi-Snf (hSwi-Snf) nucleosome remodeling complexes in solution. This information is then used to locate hSwi-Snf complexes bound to mouse mammary tumor virus promoter nucleosomal arrays, a natural target of hSwi-Snf action, in solution topographic AFM images of surface-tethered arrays. By comparing the same individual chromatin arrays before and after hSwi-Snf activation, remodeling events on these arrays can be monitored in relation to the complexes bound to them. Remodeling is observed to be: inherently heterogeneous; nonprocessive; able to occur near and far from bound complexes; often associated with nucleosome height decreases. These height decreases frequently occur near sites of DNA release from chromatin. hSwi-Snf is usually incorporated into nucleosomal arrays, with multiple DNA strands entering into it from various directions, + or - ATP; these DNA paths can change after hSwi-Snf activation. hSwi-Snf appears to interact with naked mouse mammary tumor virus DNA somewhat differently than with chromatin and ATP activation of surface-bound DNA/hSwi-Snf produces no changes detectable by AFM.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Chromatin / chemistry
  • Chromatin / metabolism*
  • Chromosomal Proteins, Non-Histone / chemistry*
  • Chromosomal Proteins, Non-Histone / metabolism
  • Chromosomes / chemistry
  • DNA / chemistry*
  • HeLa Cells
  • Humans
  • Mammary Tumor Virus, Mouse / genetics*
  • Microscopy, Atomic Force / methods*
  • Nuclear Proteins / chemistry
  • Nucleosomes / metabolism
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Tertiary
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism

Substances

  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • Nuclear Proteins
  • Nucleosomes
  • Transcription Factors
  • Adenosine Triphosphate
  • DNA