Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber

Abstract

In eukaryotic cells, DNA is wrapped around histones to form nucleosomes, which are further organized into the 30-nm chromatin fiber. A single-molecule study with homogeneous chromatin fibers now shows that the chromatin fiber behaves as a simple spring, stretching up to three times in response to pulling, a behavior indicative of a one-start helix structure. Linker histones stabilize the fiber but do not make it stiffer. The compaction of eukaryotic DNA into chromatin has been implicated in the regulation of all DNA processes. To unravel the higher-order folding of chromatin, we used magnetic tweezers and probed the mechanical properties of single 197-bp repeat length arrays of 25 nucleosomes. At forces up to 4 pN, the 30-nm fiber stretches like a Hookian spring, resulting in a three-fold extension. Together with a high nucleosome-nucleosome stacking energy, this points to a solenoid as the underlying topology of the 30-nm fiber. Unexpectedly, linker histones do not affect the length or stiffness of the fiber but stabilize its folding. Fibers with a nucleosome repeat length of 167 bp are stiffer, consistent with a two-start helical arrangement. The observed high compliance causes extensive thermal breathing, which forms a physical basis for the balance between DNA condensation and accessibility.