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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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DNA flexibility regulates transcription factor binding to nucleosomes.

Luca Mariani1, Xiao Liu1,2, Kwangwoon Lee1,3

  • 1Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115.

Biorxiv : the Preprint Server for Biology
|October 28, 2024
PubMed
Summary

Pioneer transcription factors initiate chromatin opening but bind only a few target sites. DNA sequence context within nucleosomes, not the factor itself, dictates where these crucial pioneer factors bind.

Keywords:
ChIP-seqDNA binding sitesDNA flexibilityPIONEAR-seqTranscription factorshigh-throughput nucleosome binding assaynucleosomespioneers

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Cell fate decisions rely on transcription factors (TFs) that bind DNA to regulate gene expression.
  • Pioneer TFs initiate chromatin opening, enabling access for other regulatory proteins.
  • Pioneer TFs bind only a fraction of their recognition sites, indicating regulatory mechanisms are at play.

Purpose of the Study:

  • To investigate the role of local DNA sequence context in regulating pioneer TF binding to nucleosomes.
  • To develop a high-throughput method for analyzing TF-nucleosome interactions.
  • To characterize the binding preferences of seven human pioneer TFs.

Main Methods:

  • Development of PIONEAR-seq, a sequencing-based biochemical assay for TF-nucleosome binding analysis.
  • High-throughput characterization of pioneer TF binding to nucleosome positioning sequences.
  • Comparison of TF binding to synthetic (Widom 601) and genomic DNA sequences within nucleosomes.

Main Results:

  • Pioneer TF binding preferences (dyad, periodic, end binding) are determined by the surrounding nucleosomal DNA sequence context.
  • The sequence context, rather than being intrinsic to the TF, dictates binding location on the nucleosome.
  • A model is proposed where nucleosomal DNA flexibility and rigidity govern pioneer TF binding sites.

Conclusions:

  • Nucleosomal DNA sequence context is a critical determinant of pioneer TF binding location.
  • Physical properties of nucleosomal DNA provide an additional layer of cis-regulatory information for TFs.
  • Understanding these interactions is key to deciphering cell fate decisions and gene regulation.