Effects of DNA supercoiling on chromatin architecture

Abstract

Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales. This supercoiling changes the properties of the DNA helix in a manner that substantially alters the binding specificity of DNA binding proteins and complexes, including nucleosomes, polymerases, topoisomerases and transcription factors. For example, transient over-wound DNA destabilises nucleosome core particles ahead of a transcribing polymerase, whereas under-wound DNA facilitates pre-initiation complex formation, transcription factor binding and nucleosome core particle association behind the transcribing polymerase. Importantly, DNA supercoiling can also dissipate through DNA, even in a chromatinised context, to influence both local elements and large chromatin domains. We propose a model in which changes in unconstrained DNA supercoiling influences higher levels of chromatin organisation through the additive effects of DNA supercoiling on both DNA-protein and DNA-nucleosome interactions. This model links small-scale changes in DNA and chromatin to the higher-order fibre and large-scale chromatin structures, providing a mechanism relating gene regulation to chromatin architecture in vivo.

Keywords: DNA supercoiling; Eukaryotic chromatin; Gene regulation; Genome architecture; Protein–DNA.

Fig. 1

DNA supercoils in chromatin. a Twist and writhe in naked DNA. Twist is a change in the number of base pairs per turn of the DNA double helix (blue bar). The minimum/maximum (min/max) values represent the highest level of over-/under-wound DNA twist possible before a forced DNA structural transition (Bryant et al. 2003). Writhe is a structural transition to a coiled helix which has a positive writhe (+) for over-wound DNA and a negative writhe (−) for under-wound DNA. Orange bars represent a barrier to the spread of DNA supercoiling. b The basics of chromatin structure. In eukaryotes DNA is bound by nucleosome core particles, interspersed by linker DNA, that form nucleosome arrays. These nucleosome arrays fold into a higher-order fibre and large-scale chromatin structures. DNA supercoiling can transmit through chromatin (orange arrows) to influence genome structure and regulation

Fig. 2

DNA supercoiling influences protein–DNA interactions at different scales of chromatin organisation. Orange arrows Dissipating supercoils. Importantly, the limit of supercoil influence is orchestrated by the properties of the higher-order and large-scale chromatin fibres

Fig. 3

Generating DNA supercoils in chromatin. a Transcription by RNA polymerase generates DNA supercoiling by the twin-domain model. In the transition from paused to active transcription the DNA transitions from relaxed (left panel) to generating over-wound DNA ahead of the transcription complex (facilitating nucleosome eviction) and under-wound DNA behind the polymerase complex (facilitating nucleosome deposition) (right panel)

Fig. 4

DNA supercoils influence DNA–protein interactions and catalytic activity. An overview of the ways over- and under- wound DNA can influence DNA structures, protein–DNA interactions and the catalytic activity of DNA binding proteins. ssDNA Single-strand DNA

Fig. 5

Transcription-generated DNA supercoils influence nucleosome array, higher-order fibre and large-scale chromatin organisation. Transcriptionally inactive chromatin has a compacted fibre structure and cytologically compact large-scale architecture. In contrast, transcriptionally active regions have an under-wound DNA structure that forms a decompacted/disrupted higher-order chromatin fibre and cytologically decompact large-scale chromatin structures. Green arrows actively transcribed genes, red arrows inactive genes. Orange arrows Under-wound DNA supercoils generated upstream of a transcribing polymerase, which are preferentially maintained at promoters and at transcriptionally active large-scale DNA supercoil domains (e.g. Naughton et al. 2013a)