DNA sequence encodes the position of DNA supercoils

The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself.

the DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific sequences.

sequence-dependent intrinsic curvature is the key determinant of pinning strength

Analysis of several prokaryotic genomes indicates that plectonemes localize directly upstream of promoters

Our findings reveal a hidden code in the genome that helps to spatially organize the chromosomal DNA.

Control of DNA supercoiling is of vital importance to cells. Torsional strain imposed by DNA-processing enzymes induces supercoiling of DNA, which triggers large structural rearrangements through the formation of plectonemes

Recent biochemical studies suggest that supercoiling plays an important role in the regulation of gene expression in both prokaryotes and eukaryotes

In order to tailor the degree of supercoiling around specific genes, chromatin is organized into independent topological domains with varying degrees of torsional strain

Domains that contain highly transcribed genes are generally underwound whereas inactive genes are overwound

Furthermore, transcription of a gene transiently alters the local supercoiling, while, in turn, torsional strain influences the rate of transcription

For many years, the effect of DNA supercoiling on various cellular processes has mainly been understood as a torsional stress that enzymes should overcome or exploit for their function. More recently, supercoiling has been acknowledged as a key component of the spatial architecture of the genome

Here, bound proteins are typically viewed as the primary determinant of sequence-specific tertiary structures while intrinsic mechanical features of the DNA are often ignored. However, the DNA sequence influences its local mechanical properties such as bending stiffness, curvature, and duplex stability, which in turn alter the energetics of plectoneme formation at specific sequences

Our findings reveal how a previously unrecognized ‘hidden code’ of intrinsic curvature governs the localization of local DNA supercoils, and hence the organization of the three-dimensional structure of the genome.

A full statistical mechanical modeling of the plectonemic structures distributed across the DNA molecule should further improve the predictive power and accuracy, but will require significant computational resources and time.

Significant intrinsic curvatures are encoded in genomic DNA, as evident in our scans of both prokaryotic and eukaryotic genomes, which indicates its biological relevance.

In addition to this direct interaction of RNA polymerase and curved DNA, our results suggest an indirect effect, as the same curved DNA can easily pin a plectoneme that can further regulate the transcription initiation and elongation by structural re-arrangement of the promotor and coding regions.

promoter sequences have evolved local regions with highly curved DNA that promote the localization of DNA plectonemes at these sites.

There may be multiple reasons for this.

For one, it may help to expose these DNA regions to the outer edge of the dense nucleoid, making them accessible to RNAP, transcription factors, and topoisomerases.

Plectonemes may also play a role in the bursting dynamics of gene expression, since each RNAP alters the supercoiling density within a topological domain as it transcribes, adding or removing nearby plectonemes

In addition, by bringing distant regions of DNA close together, plectonemes may influence specific promoter-enhancer interactions to regulate gene expression

Finally, plectoneme tips may help RNA polymerase to initiate transcription, since the formation of an open complex also requires bending of the DNA, a mechanism that was proposed as a universal method of regulating gene expression across all organisms

Our analysis of eukaryotic genomes showed a greater diversity of behavior. The spacing of the peaks suggests that plectonemes may play a role in positioning nucleosomes, consistent with proposals that nucleosome positioning may rely on sequence-dependent signals near promoters

The plectoneme signal encoded by intrinsic curvature could therefore indirectly position the promoter plectoneme tip by helping to organize these nearby nucleosomes.

The above findings demonstrate that DNA contains a previously hidden ‘code’ that determines the local intrinsic curvature and consequently governs the locations of plectonemes. These plectonemes can organize DNA within topological domains, providing fine-scale control of the three-dimensional structure of the genome

it will be interesting to explore how changes in this plectoneme code affect levels of gene expression and other vital cellular processes.