Analysis of the overlapping tri-nucleosome association with genomic and synthetic DNA

Nucleosome consists of a histone octamer wrapped by 145 bps of DNA and serves as a fundamental unit of chromatin. The overlapping di-nucleosome (OLDN) is found as another chromatin unit, in which 250 bps of DNA continuously wraps around the intimately associated histone octamer-hexamer complex. In the present study, our genome-wide analysis found a higher nucleosome stacking structure, overlapping tri-nucleosome (OLTN), in which about 350 bps of DNA wrap around the histone octamer-hexamer-hexamer complex. We quantified the length of DNA associated with the 20-mer histone core, and also we found that the OLTN localizes downstream of the transcription start sites as well as the OLDN does. The results suggest that nucleosome stacking structures may be formed for gene regulation. Overall design: MNase-seq of presumable fragments of OLTN, OLDN, and nucleosome using HeLa cell genomic DNA and synthetic DNA