DNA Supercoiling, Topoisomerases, and Cohesin: Partners in Regulating Chromatin Architecture?

Abstract

Although our knowledge of chromatin organization has advanced significantly in recent years, much about the relationships between different features of genome architecture is still unknown. Folding of mammalian genomes into spatial domains is thought to depend on architectural proteins, other DNA-binding proteins, and different forms of RNA. In addition, emerging evidence points towards the possibility that the three-dimensional organisation of the genome is controlled by DNA topology. In this scenario, cohesin, CCCTC-binding factor (CTCF), transcription, DNA supercoiling, and topoisomerases are integrated to dictate different layers of genome organization, and the contribution of all four to gene control is an important direction of future studies. In this perspective, we review recent studies that give new insight on how DNA supercoiling shape chromatin structure.

Keywords: CTCF; DNA topology; cohesin; genome organization; topoisomerase; transcription.

Figure 1

Whole-genome chromatin conformation capture (Hi-C) detect chromosomal rearrangements. Overview of the Hi-C method. Briefly, cells are first treated with formaldehyde, which crosslinks chromatin segments that are spatially adjacent. The crosslinked chromatin is thereafter digested with restriction enzyme(s). The resulting DNA fragments are labelled with biotinylated nucleotides and subjected to ligation. Crosslinks are reversed, DNA sheared, and biotinylated fragments are isolated using streptavidin beads. Finally, deep sequencing of the purified fragments identifies which chromosomal regions were in proximity at the time of formaldehyde cross-linking. Recently, the resolution of Hi-C has been improved by replacing restriction enzyme cleavage with micrococcal nuclease (MNase) digestion [23], or using in situ Hi-C, in which DNA-DNA proximity ligation is performed in intact nuclei [24].

Figure 2

The 3D genome and factors contributing to its organization. (A) In the nucleus interphase, chromosomes are organized in A/B compartments, which in turn contain topologically associating domains (TADs) and sub-TADs; (B) Models for domain formation by cohesin as a loop extruding factor; (C) Transcription-generated supercoiling can contribute to TADs structure. Positive supercoiling generated ahead of the moving RNA polymerase (RNAP) could promote cohesin sliding along the DNA until the complex meets an obstacle such as CTCF or, possibly, another region of supercoiled DNA. Negative supercoiling favours loop formation and stabilization of promoter-enhancer interactions.

Figure 3

Supercoiling contributes to loop formation. (A) Supercoiled DNA folds into plectonemic (left) or toroidal (right) conformations. While plectonemic structures have been observed in bacterial chromosomes, toroidal supercoils are found constrained within nucleosomes. Here, both cartoons depict negative supercoils. For a detailed description of DNA topology, please see [53]; (B) Topoisomerase activity is regulated to ensure that negative supercoiling is maintained along transcribed units. Positive supercoils accumulate in front of the polymerase.