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DNA bendability regulates transcription factor binding to nucleosomes.

Luca Mariani1, Xiao Liu2,3,4, Kwangwoon Lee2,5,6

  • 1Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. lmariani@bwh.harvard.edu.

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Pioneering transcription factors (TFs) control cell fates by binding DNA. A new method, PIONEAR-seq, reveals that nucleosome sequence context, not just TF motifs, regulates this crucial pioneer binding.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Epigenetics

Background:

  • Cell fate determination relies on pioneer transcription factors (TFs).
  • Pioneer TFs bind specific DNA sequences within nucleosomes.
  • The limited occupancy of recognition sites suggests sequence context influences pioneer binding.

Purpose of the Study:

  • To develop a high-throughput assay for characterizing pioneer transcription factor binding to nucleosomes.
  • To investigate the role of nucleosome sequence context in regulating pioneer binding.
  • To propose a model for how DNA sequence bendability within nucleosomes positions pioneer binding.

Main Methods:

  • Development of PIONEAR-seq, a high-throughput biochemical assay.
  • Assay of 11 human TFs binding to nucleosomes using Widom 601 and genomic DNA sequences.
  • Analysis of TF binding patterns in relation to nucleosome structure and DNA sequence context.

Main Results:

  • Pioneer binding is primarily mediated by TF recognition motifs but significantly regulated by the broader nucleosome sequence context.
  • Genomic sequences revealed different binding patterns (end binding) compared to synthetic sequences (dyad or periodic binding) for certain TFs.
  • Evidence suggests local DNA bendability within nucleosomes influences pioneer TF positioning.

Conclusions:

  • Nucleosome sequence context is a critical regulatory layer for pioneer transcription factor binding.
  • DNA sequence bendability within nucleosomes plays a role in positioning pioneer TFs.
  • This finding adds a new cis-regulatory mechanism to our understanding of eukaryotic genome regulation and cell fate control.