High-resolution whole-genome analysis of sister-chromatid cohesion

Barre, François Xavier; Espinosa, Elena; Paly, Evelyne

doi:10.1101/2019.12.17.879379

Cited by 2 publications

(1 citation statement)

References 42 publications

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“…Hi-C is a popular method to study chromosome conformation, and a derivative to track intersister contacts was recently designed in eukaryotes (Oomen et al, 2020). The use of loxP recombination to reveal proximity of sisters (Lesterlin et al, 2012) or their catenation (Mariezcurrena and Uhlmann, 2017) is also a powerful tool to decipher local chromosome topology, with a genome-wide loxP recombination based assay recently adapted to survey sister proximity in V. cholera (Espinosa et al, 2019). Our results suggest that Hi-C can also offer a read-out of topological constraints.…”

Section: Discussionmentioning

confidence: 99%

Genomic contacts reveal the control of sister chromosome decatenation in E. coli

Billault-Chaumartin

et al. 2021

Preprint

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In bacteria, chromosome segregation occurs progressively, from the origin to the terminus, a few minutes after the replication of each locus. In-between replication and segregation, sister loci are maintained in an apparent cohesive state by topological links. Whereas topoisomerase IV (Topo IV), the main bacteria decatenase, controls segregation, little is known regarding the influence of the cohesion step on chromosome folding. In this work, we investigated chromosome folding in cells with altered decatenation activities. Within minutes after Topo IV inactivation, a massive chromosome reorganization takes place, associated with increases in trans-contacts between catenated sister chromatids and in long-range cis-contacts between the terminus and distant loci on the genome. A genetic analysis of these signals allowed us to decipher specific roles for Topo IV and Topo III, an accessory decatenase. Moreover we revealed the role of MatP, the terminus macrodomain organizing system and MukB, the E. coli SMC in organizing sister chromatids tied by persistent catenation links . We propose that large-scale conformation changes observed in these conditions reveal a defective decatenation hub located in the terminus area. Altogether, our findings support a model of spatial and temporal partition of the tasks required for sister chromosome segregation.

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Section: Discussionmentioning

confidence: 99%

Genomic contacts reveal the control of sister chromosome decatenation in E. coli

Billault-Chaumartin

et al. 2021

Preprint

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Detecting chromatin interactions along and between sister chromatids with SisterC

Oomen

Hedger

Watts

et al. 2020

Preprint

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Accurate chromosome segregation requires chromosome compaction with concordant disentanglement of the two sister chromatids. This process has been studied extensively by microscopy but has remained a challenge for genomic methods, such as Hi-C, because sister chromatids have identical DNA sequences. Here we describe SisterC, a chromosome conformation capture assay that can distinguish interactions between and within sister chromatids. The assay is based on BrdU incorporation during Sphase, which labels the newly replicated strands of the sister chromatids. This is followed by Hi-C, e.g. during different stages of mitosis, and the selective destruction of BrdU containing strands by UV/Hoechst treatment. After PCR amplification and sequencing of the remaining intact strands, this allows for the assignment of Hi-C products as inter-and intra-sister interactions by read orientation. We performed SisterC on mitotically arrested S. cerevisiae cells. As expected, we find prominent interactions and alignment of sister chromatids at their centromeres. Along the arms, sister chromatids are less precisely aligned with inter-sister connections every ~35kb. In many instances, inter-sister interactions do not involve the interaction of two identical loci but occur between cohesin binding sites that can be offset by 5 to 25kb. Along sister chromatids, extruding cohesin forms loops up to 50kb. Combined, SisterC allows the observation of the complex interplay between sister chromatid compaction and sister chromatid segregation as the cell transitions from late S-phase to mitosis. SisterC should be applicable to study mitotic events in a wide range of organisms and cell types.During S-phase, when sister chromatids are formed, they are closely cohesed by the cohesin complex. Sister chromatids are initially also thought to be wrapped around each other and entangled.During the subsequent mitosis, sister chromatids become compacted and, in the process, become disentangled and segregated from each other, although they remain aligned side by side 1 . Classically, this process has been studied using microscopic methods by labeling sister chromatids differently using thymidine analogues 2,3 . It has been difficult to study this complex series of mitotic events using genomic techniques such as Hi-C, as sequencing-based methods cannot distinguish the identical sister chromatids, and therefore cannot differentiate interactions between and along sister chromatids. Recently an assay detecting sister chromatid exchange events allowed mapping of sister chromatid interactions genome wide in bacteria 4 . However, this approach requires extensive genome editing to introduce sister chromatid exchange markers throughout the genome.Here we present a Hi-C-based assay, SisterC, that can detect and distinguish inter-and intrasister interactions. We demonstrate the performance of the assay by studying mitotic S. cerevisiae cells.In S. cerevisiae the cohesin complex mediates inter-sister interactions at the centromere and along the chromosome arms ("cohesi...

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High-resolution whole-genome analysis of sister-chromatid cohesion

Cited by 2 publications

References 42 publications

Genomic contacts reveal the control of sister chromosome decatenation in E. coli

Genomic contacts reveal the control of sister chromosome decatenation in E. coli

Detecting chromatin interactions along and between sister chromatids with SisterC

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