DNA bendability regulates transcription factor binding to nucleosomes.

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.