Superstructural features of the upstream regulatory regions of two pea rbcS genes and nucleosomes positioning: Theoretical prediction and experimental evaluation

Nucleosome positioning on two 384 bp DNA. fragments, obtained from the upstream regulatory region of two pea rbcS genes, relevant in photoregulated transcription, was predicted using our theoretical method, based on the evaluation of the sequence dependent DNA bending energy. The theoretical prediction was checked by experimental evaluation of nucleosome positions after in vitro reconstitution, by mapping Exonuclease III-resistant borders and by digesting monomeric sequences with various restriction enzymes. Both approaches satisfactorily confirmed the theoretical predictions, showing that the nucleotide sequence intrinsic bendability has a dominant role in nucleosome positioning.