TY - JOUR T1 - Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae A1 - Wang, Ji-Ping A1 - Fondufe-Mittendorf, Yvonne A1 - Xi, Liqun A1 - Tsai, Guei-Feng A1 - Segal, Eran A1 - Widom, Jonathan Y1 - 2008/09/12 N2 - Author Summary Eukaryotic genomic DNA exists as chromatin, with the DNA wrapped locally into a repeating array of protein–DNA complexes (“nucleosomes”) separated by short stretches of unwrapped “linker” DNA. Nucleosome arrays further compact into ∼30-nm-wide higher-order chromatin structures. Despite decades of work, there remains no agreement about the structure of the 30 nm fiber, or even if the structure is ordered or random. The helical symmetry of DNA couples the one-dimensional distribution of nucleosomes along the DNA to an intrinsic three-dimensional structure for the chromatin fiber. Random linker length distributions imply random three-dimensional intrinsic fiber structures, whereas different possible nonrandom length distributions imply different ordered structures. Here we use two independent computational methods, with two independent kinds of experimental data, to experimentally define the probability distribution of linker DNA lengths in yeast. Both methods agree that linker DNA lengths in yeast come in a set of preferentially quantized lengths that differ one from another by ∼10 bp, the DNA helical repeat, with a preferred phase offset of 5 bp. The preferential quantization of lengths implies that the intrinsic three-dimensional structure for the average chromatin fiber is ordered, not random. The 5 bp offset implies a particular geometry for this intrinsic structure. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 4 IS - 9 UR - https://doi.org/10.1371/journal.pcbi.1000175 SP - e1000175 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1000175 ER -