Human Smc5/6 recognises transcription-generated positive DNA supercoils

Abstract

Beyond its essential roles in ensuring faithful chromosome segregation and genomic stability, the human Smc5/6 complex acts as an antiviral factor. It binds to and impedes the transcription of extrachromosomal DNA templates; an ability which is lost upon chromosomal DNA integration. How the complex distinguishes among different DNA templates is unknown. Here we show that, in human cells, Smc5/6 preferentially binds to circular rather than linear extrachromosomal DNA. We further show that this binding is unlikely due to differences in the chromatin composition. Instead, the transcriptional process, per se, and more specifically the accumulation of DNA secondary structures known to be substrates for topoisomerases, is responsible for Smc5/6 recruitment. Those findings, in conjunction with our genome-wide Smc5/6 binding analysis showing that Smc5/6 localizes at few but highly transcribe chromosome loci, reveal a previously unforeseen role of Smc5/6 in DNA topology management during transcription.

All eukaryotic SMC proteins induce a twist of -0.6 at each DNA-loop-extrusion step

“…The latter could explain how cohesin may drive transcription of enhancer-controlled developmental genes even in the absence of loop anchors positioned at enhancer-promoter pairs( 10 ). SMCs preferentially bind and loop onto positively over negatively supercoiled DNA ( 23, 24, 71 ), which could prevent SMCs to load onto already extruded (negatively supercoiled) extruded loops. This bias could contribute to the appearance of characteristic CTCF-dependent TAD corner dots in Hi-C maps ( 57, 72, 73 ) since those depend on a fraction of TADs whose DNA is completely contained in SMC-mediated loops ( 74 ) as observed in vivo ( 75, 76 ).…”

The SMC5/6 complex: folding chromosomes back into shape when genomes take a break

“…Recently, the loop extrusion activity of SMC5/6 complex has also been observed during transcription. Single-molecule imaging and Hi-C analyses show that SMC5/6 complex dimers can recognize and link chromosomal regions containing positively supercoiled DNA especially during transcription, and initiate loop extrusion to fold the supercoiled DNA into large plectonemic loops for three-dimensional organization of chromosomes ( 138 , 139 ).…”

SMC-based immunity against extrachromosomal DNA elements

“…The viral DNA targeted by Smc5/6 is thought to be extrachromosomal ( Figure 3C ): unintegrated elements of HIV [ 60 ], the circular episome of KSHV [ 61 ], and covalently closed circular DNA (cccDNA) of HBV [ 57 , 58 ]. Like in Wadjet, the restriction of extrachromosomal DNA appears to be sequence-independent and limited to circular DNA molecules [ 63 , 65 ]. In contrast with Wadjet, however, DNA helical topology has been suggested to play a crucial role.…”

“…In contrast with Wadjet, however, DNA helical topology has been suggested to play a crucial role. Accordingly, human Smc5/6 is proposed to recognize positively supercoiled DNA generated during transcription of extrachromosomal circular DNA [ 65 ]. How such a topological signal is limited to extrachromosomal DNA however remains enigmatic.…”