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#nucleosome positioning

2 public questions tagged with this topic.

Regulation of chromatin structure

What happens if two DNA-binding proteins bind closer than 147 bp?

Nucleosome formation requires approximately 147 base pairs of DNA wrapping 1.65 turns around histone octamer plus accessible linker. When sequence-specific DNA binding proteins occupy sites less than this distance apart, steric hindrance prevents octamer deposition because binding proteins block wrapping path and compete for major groove contacts. In vitro reconstitution shows that tight clustering of transcription factors, insulators or polymerases creates nucleosome-depleted regions, while cooperative positioning can generate phased arrays adjacent to barriers. This principle underlies promoter architecture where regulatory factor clusters maintain open chromatin for transcriptional initiation.

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 4: Nucleosome Positioning and Barrier Models

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Regulation of chromatin structure

Which DNA feature favors nucleosome positioning?

Genome-wide nucleosome positioning maps reveal sequence features influencing octamer affinity. Experimental SELEX and computational models show DNA sequences where AT-rich minor grooves face inward compress more easily, alternating AT/GC every five base pairs, approximately half helical turn, aligns flexible pyrimidine-purine steps with curvature required around histone, reducing elastic energy cost of wrapping stiff DNA. Poly-A tracts rigid and intrinsically curved disfavor nucleosomes acting as excluding signals, random sequence intermediate, pure GC stretches less bendable. Periodic AT/GC pattern predicts nucleosome occupancy, positioning at promoters and transcription start site depletion, guiding transcriptional regulation across eukaryotic genomes.

Ref: Satchwell et al., J Mol Biol 1986; Segal et al., Nature 2006: DNA Feature Favoring Nucleosome Positioning AT/GC Periodicity

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