Supercoiling in DNA and chromatin

Abstract

Supercoiling is a fundamental property of DNA and chromatin. It is modulated by polymerase and topoisomerase activities and, through regulated constraint, by DNA/chromatin binding proteins. As a non-covalent and elusive topological modification, supercoiling has proved intractable to research despite being a crucial regulator of nuclear structure and function. Recent studies have improved our understanding of the formation, regulation and organisation of supercoiling domains in vivo, and reinforce the prospect that the propagation of supercoiling can influence local and global chromatin structure. However, to further our understanding the development of new experimental tools and models are required to better dissect the mechanics of this key topological regulator.

Figure 1

(a) Twin domain model of DNA supercoiling. A transcribing polymerase generates positive supercoiling ahead and negative supercoiling behind. (b) Likewise, during replication the polymerase introduces positive supercoiling ahead whilst in contrast the newly replicated strands of DNA are in a relaxed configuration.

Figure 2

(a) Biotinylated-psoralen (bTMP) intercalates into the DNA helix preferentially at negatively supercoiled regions. bTMP binding, as a measure of DNA supercoiling, was mapped across a segment of chromosome 11 revealing the presence of underwound and overwound supercoiling domains (modified from Naughton et al. [24^••]). (b) The sequences defining supercoiling domain boundaries and topology boundaries [22] partially overlap but indicate that different factors must be responsible. (c) Organisation of prokaryotic genomes into large structural domains with architectural boundaries (orange spots) but subdivided into smaller supercoiling domains. (d) Eukaryotic genomes are similarly organised into large structural domains delimited by CTCF rich boundaries (orange spots) and divided into many smaller supercoiling domains.

Figure 3

(a) Transcriptional activation of MYC is accompanied by a SWI/SNF activity revealing the FUSE element. A build up of negative supercoiling propagates along the fibre, melting the FUSE element promoting the binding of the ssDNA binding proteins, FBP and FIR [33,48]. (b) Negative supercoiling promotes ssDNA patch formation allowing the mutagenic activity of activation-induced cytidine deaminase (AID) [35^•].

Figure 4

Model representing how changes in supercoiling could influence the structure of the 30-nm chromatin fibre. Here twist is shown to cause the fibre to over-wind or under-wind altering its tertiary conformation and potentially enabling the torsional stress to be propagated to distant sites.