Chromosome length influences replication-induced topological stress

Abstract

During chromosome duplication the parental DNA molecule becomes overwound, or positively supercoiled, in the region ahead of the advancing replication fork. To allow fork progression, this superhelical tension has to be removed by topoisomerases, which operate by introducing transient DNA breaks1. Positive supercoiling can also be diminished if the advancing fork rotates along the DNA helix, but then sister chromatid intertwinings form in its wake1,2. Despite these insights it remains largely unknown how replication-induced superhelical stress is dealt with on linear, eukaryotic chromosomes. Here we show that this stress increases with the length of Saccharomyces cerevisiae chromosomes. This highlights the possibility that superhelical tension is handled on a chromosome scale and not only within topologically closed chromosomal domains as the current view predicts. We found that inhibition of type I topoisomerases leads to a late replication delay of longer, but not shorter, chromosomes. This phenotype is also displayed by cells expressing mutated versions of the cohesin- and condensin-related Smc5/6 complex. The frequency of chromosomal association sites of the Smc5/6 complex increases in response to chromosome lengthening, chromosome circularization, or inactivation of topoisomerase 2, all having the potential to increase the number of sister chromatid intertwinings3. Furthermore, non-functional Smc6 reduces the accumulation of intertwined sister plasmids after one round of replication in the absence of topoisomerase 2 function. Our results demonstrate that the length of a chromosome influences the need of superhelical tension release in Saccharomyces cerevisiae, and allow us to propose a model where the Smc5/6 complex facilitates fork rotation by sequestering nascent chromatid intertwinings that form behind the replication machinery.

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Figure 1: Top1, Top3 and Smc5/6 are required for timely completion of replication on long chromosomes.
Figure 2: Inactivation of Top2, but not Top1, increases the frequency of Smc6 chromosomal interactions.
Figure 3: The Smc5/6 complex senses chromosome length and circularization of Chr III.
Figure 4: The Smc5/6 complex facilitates catenation of an episomal plasmid.

Accession codes

Primary accessions

Gene Expression Omnibus

Sequence Read Archive

Data deposits

Original data files from ChIP-sequencing experiments can be found at http://trace.ncbi.nlm.nih.gov/Traces/sra/, accession number SRP004920, and from ChIP-on-chip experiments at http://www.ncbi.nlm.nih.gov/geo/, accession number GSE26263.

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Acknowledgements

We thank K. Nasmyth, J. Haber, E. Green and X. Zhao for yeast strains and the BEA core facility at Karolinska Institutet for help with ChIP on chip. Financial support: Strategic Japanese-Swedish Cooperative Program from JST, SSF and Vinnova (C.S. and K.S.); please see Supplementary Information for additional support.

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A.K. performed the PFGE-based assays; A.K. and T.K. the plasmid assays; A.K., H.B.-L. and K.J. the ChIP-on-chip; K.J., Y.K. and K.S. the ChIP sequencing. T.I. and K.S. carried out the computational analysis and C.S. the segregation experiment. H.B.-L., L.S., K.S. and C.S. initiated the study, A.K., K.S. and C.S. continued and finalized its design. A.K. and C.S. wrote the paper. All authors analysed data, discussed the results and commented on the manuscript.

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Correspondence to Camilla Sjögren.

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The authors declare no competing financial interests.

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The file contains Supplementary Text, Supplementary Tables 1-2, Supplementary Figures 1-11 and additional references. (PDF 1704 kb)

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Kegel, A., Betts-Lindroos, H., Kanno, T. et al. Chromosome length influences replication-induced topological stress. Nature 471, 392–396 (2011). https://doi.org/10.1038/nature09791

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