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Native nucleosome-positioning elements as alternatives to the 601 sequence for nucleosome repositioning studies.

Ruo-Wen Chen1, Shane D Stoeber2, Ilana M Nodelman3

  • 1Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, OH 43210, United States.

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|September 9, 2025
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Researchers developed native nucleosome-positioning elements (NPEs) from yeast to study DNA sequence effects on nucleosome repositioning. These native NPEs enable transcription factor-mediated repositioning, unlike the artificial 601 sequence.

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • Chromatin Structure

Background:

  • Nucleosome repositioning is crucial for gene transcription initiation.
  • The Widom 601 sequence is a common tool for positioning nucleosomes but is artificial.
  • Native DNA sequences are needed to understand in vivo nucleosome dynamics.

Purpose of the Study:

  • To characterize native nucleosome-positioning elements (NPEs) from yeast.
  • To evaluate the utility of native NPEs in biochemical studies of nucleosome repositioning.
  • To compare the behavior of nucleosomes with native NPEs versus the 601 sequence.

Main Methods:

  • Characterization of nucleosome position distributions and formation free energies.
  • Biochemical assays using transcription factors (TFs) and the chromatin remodeler Chd1.
  • Comparative analysis of nucleosome repositioning on native NPEs and the 601 sequence.

Main Results:

  • Native NPEs from Saccharomyces cerevisiae were characterized.
  • Transcription factors could reposition nucleosomes containing native NPEs, but not those with the 601 sequence.
  • Nucleosome unwrapping and Chd1 remodeling rates showed similarities between native NPEs and the 601 sequence.

Conclusions:

  • Native NPEs serve as a viable alternative to the 601 sequence for studying nucleosome repositioning.
  • Native NPEs facilitate the investigation of DNA sequence roles in TF-mediated nucleosome dynamics.
  • This study provides a valuable toolset for exploring native chromatin structures and their regulation.