Supercoiling biases the formation of loops involved in gene regulation

Abstract

The function of DNA as a repository of genetic information is well-known. The post-genomic effort is to understand how this information-containing filament is chaperoned to manage its compaction and topological states. Indeed, the activities of enzymes that transcribe, replicate, or repair DNA are regulated to a large degree by access. Proteins that act at a distance along the filament by binding at one site and contacting another site, perhaps as part of a bigger complex, create loops that constitute topological domains and influence regulation. DNA loops and plectonemes are not necessarily spontaneous, especially large loops under tension for which high energy is required to bring their ends together, or small loops that require accessory proteins to facilitate DNA bending. However, the torsion in stiff filaments such as DNA dramatically modulates the topology, driving it from extended and genetically accessible to more looped and compact, genetically secured forms. Furthermore, there are accessory factors that bias the response of the DNA filament to supercoiling. For example, small molecules like polyamines, which neutralize the negative charge repulsions along the phosphate backbone, enhance flexibility and promote writhe over twist in response to torsion. Such increased flexibility likely pushes the topological equilibrium from twist toward writhe at tensions thought to exist in vivo. A predictable corollary is that stiffening DNA antagonizes looping and bending. Certain sequences are known to be more or less flexible or to exhibit curvature, and this may affect interactions with binding proteins. In vivo all of these factors operate simultaneously on DNA that is generally negatively supercoiled to some degree. Therefore, in order to better understand gene regulation that involves protein-mediated DNA loops, it is critical to understand the thermodynamics and kinetics of looping in DNA that is under tension, negatively supercoiled, and perhaps exposed to molecules that alter elasticity. Recent experiments quantitatively reveal how much negatively supercoiling DNA lowers the free energy of looping, possibly biasing the operation of genetic switches.

DNA fluctuations reveal the size and dynamics of topological domains

“…Importantly, plectonemes spatially juxtapose sites that are distant in linear DNA sequence and, therefore, enable bridging and looping of DNA by proteins that engage multiple binding sites. Proteininduced conformational changes and separation of topological domains in DNA, in turn, provide another critical level of genomic regulation (6,(9)(10)(11)(12)(13)(14). A large body of experimental and computational research has resulted in a quantitative understanding of the average geometry of supercoiled DNA under a range of environmental conditions (7,(14)(15)(16)(17)(18)(19)(20)(21)(22).…”

Free Energy Landscape and Dynamics of Supercoiled DNA by High-Speed Atomic Force Microscopy

“…7,8 Writing ΔWr occurs in the form of plectonemes, an interwound con-formation of double-helical DNA, which enhances the target search of site-specific DNA-binding proteins 9 as well as protein-mediated loop formation. 10 Thus, organizing the genome in topological domains infers regulatory control over gene expression via DNA supercoiling. Consequently, the properties of DNA supercoiling have been intensively studied.…”

“…DNA is supercoiled when Lk differs from the energetically most favorable value Lk 0 and the linking difference Δ Lk = Lk – Lk 0 can be expressed in terms of deviations in twist Δ T w and writhe Δ Wr from their equilibrium values (Δ Lk = Δ Tw + Δ Wr ). Twist deformations Δ T w affect formation of melting bubbles, cruciform, or Z-DNA and can modulate protein binding. , Writing Δ Wr occurs in the form of plectonemes, an interwound conformation of double-helical DNA, which enhances the target search of site-specific DNA-binding proteins as well as protein-mediated loop formation . Thus, organizing the genome in topological domains infers regulatory control over gene expression via DNA supercoiling.…”

Meeting report – NSF-sponsored workshop ‘Progress and Prospects of Single-Molecule Force Spectroscopy in Biological and Chemical Sciences’

“…In addition, RNAP pausing at obstacles depends not only on the amplitude, but also on the directionality of the tension applied to the DNA template. Finally, she showed that the strength of a protein roadblock is increased if the protein bridges two distant sites, thus mediating a DNA loop (Finzi and Dunlap, 2016). In conclusion, looping might convert a weak protein-binding site into a strong roadblock for transcription, indicating new means of transcription regulation.…”