Practice question

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.