Dynamic regulation of transcription factors by nucleosome remodeling

Elife. 2015 Jun 5:4:e06249. doi: 10.7554/eLife.06249.

Abstract

The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes.

Keywords: S. cerevisiae; biochemistry; biophysics; chromatin remodeling; gene regulation; optical trapping; single molecule studies; structural biology; transcription factor.

Publication types

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

MeSH terms

  • Adenosine Triphosphatases / metabolism*
  • Chromatin Assembly and Disassembly / physiology
  • Chromosomal Proteins, Non-Histone / metabolism*
  • DNA / chemistry
  • DNA-Binding Proteins / metabolism*
  • Models, Biological*
  • Nucleosomes / physiology*
  • Optical Tweezers
  • Plasmids / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*

Substances

  • Chromosomal Proteins, Non-Histone
  • DNA-Binding Proteins
  • Nucleosomes
  • SWI-SNF-B chromatin-remodeling complex
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • DNA
  • Adenosine Triphosphatases
  • ISW1 protein, S cerevisiae