Abstract
Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. However, the propagation of twist in condensed chromatin remains yet unresolved. Here, we measure how force and torque impact chromatin fibers with a nucleosome repeat length of 167 and 197. We find that both types of fibers fold into a left-handed superhelix that can be stabilized by positive torsion. We observe that the structural changes induced by twist were reversible, indicating that chromatin has a large degree of elasticity. Our direct measurements of torque confirmed the hypothesis of chromatin fibers as a twist buffer. Using a statistical mechanics-based torsional spring model, we extracted values of the chromatin twist modulus and the linking number per stacked nucleosome that were in good agreement with values measured here experimentally. Overall, our findings indicate that the supercoiling generated by DNA-processing enzymes, predicted by the twin-supercoiled domain model, can be largely accommodated by the higher-order structure of chromatin.
Highlights
Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases
We studied torsional properties of chromatin fibers reconstituted on tandem repeats of 601-DNA sequences (30Á167 bp and 25Á197 bp) flanked by 2030 bp nucleosome-free DNA handles
The samples were tethered at either end by multiple bonds to a magnetic bead or to the surface of a flow cell, respectively, in order to constrain their overall linking number (Fig. 1b) and to capture the structural dynamics of chromatin fibers under torsion
Summary
Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. A primary regulator of gene expression is supercoiling, the over- or under-twisting of the right-handed DNA double helix (relative to its canonical 10.4 base pairs per helical turn26) that results from bending or unwinding of DNA during replication or transcription During the latter process, RNA polymerase (RNAp) generates large torsional stresses at rates up to seven DNA supercoils per second[27]. A genome-wide study of the supercoiling density within large topological domains showed that overwound and underwound regions differed in the degree of chromatin compaction[32]: actively transcribed, gene-rich loci were typically found to be underwound yet less compacted relative to transcriptionally silent regions of densely packed chromatin This complex interplay between transcription, supercoiling, and chromatin compaction has been investigated at a mechanistic level only in the context of individual nucleosomes[33]. It remains unknown how torsional stress affects the compact chromatin fibers formed by multiple interacting nucleosomes
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