The Handedness of Nucleosomes is Governed by the Supercoiling of DNA

Abstract

In eukaryotic cells, histone proteins constitute the basic building blocks for higher chromatin structures by forming a nucleosome where DNA wraps around a histone octamer. While it is widely accepted that the DNA is wound in left-handed manner around the histone core, recent experimental evidence supports the existence of right-handed nucleosomes in vivo and in vitro, especially for histone variant nucleosomes such as the centromere-specific histone variant CENP-A/CENH3. Furthermore, newer studies using high throughput sequencing demonstrated that large chromosomal domains exist with alternative topological states in vivo. Thus, how such states can support the left-handed octamer remains unknown.Here, we use magnetic tweezers to examine chaperone-mediated nucleosome assembly, for canonical H3 and histone variant CENP-A nucleosomes, under various DNA supercoiling states. To our surprise, positive and negative DNA supercoiling applied to the DNA prior to nucleosome assembly, can be readily absorbed by H3 and CENP-A nucleosomes. Indeed, we observe that positive supercoiling of the DNA preceding assembly leads to the formation of right-handed H3 and CENP-A nucleosomes. Conversely, negative supercoiling of DNA results in left-handed H3 and CENP-A nucleosomes.These data support decades-old findings that nucleosomes with both types of chirality exist, and could potentially resolve controversy in recent literature surrounding the topological state of CENP-A nucleosomes in vivo. Finally, our observations have the important biological implication that individual nucleosomes can adapt their handedness as an adaptive feature in response to topological stress applied upon the DNA by biological forces such as transcription, replication, and mitosis. Our data support the possibility that excess supercoiling in large chromosomal domains may be relaxed through adaptive transformation of chirality embedded within the core of nucleosomes, and that this unusual facet of nucleosome behavior may underlie a general feature of the chromatin organization.