pBSK-Zeo-5S-G5E4 (p5S) acceptor plasmids used in the work. The 2.56 kb 5S-G5E4 fragment DNA for polynucleosome assembly (PN) was previously described  and was cloned into the pBSP-zeo vector (A). This fragment is made of two times five repeats of 5S sequences surrounding a central sequence containing five gal4 DNA binding sites and the adenovirus 2 E4 minimal promoter. The p5S vector thus contains a region 1 containing nucleosome-positioning sequences and a region 2 containing the pBSK-zeo backbone. Each 5S fragment is separated by two EcoRI restriction sites. Nucleosome occupancy prediction performed using the method previously described by  and used in  indicates the formation on the chromatinized vector of two regions with different chromatin organization (regular and stable nucleosomes in the 5S-G5E4 region 1 and less organized and stable nucleosomes in the pBSK-Zeo backbone region 2 (B). Restriction inhibition assay demonstrates that the two regions are not equally accessible since region 1 is highly protected when chromatinized whereas region 2 remains highly accessible for restriction site cutting even in the nucleosomal structure (see Additional file 1: Figure S1).