Genome-wide mapping of sister chromatid exchange events in single yeast cells using Strand-seq

Claussin, Clémence; Porubský, David; Spierings, Diana C.J.; Halsema, Nancy; Rentas, Stefan; Guryev, Victor; Lansdorp, Peter M; Chang, Michael

doi:10.7554/elife.30560

Cited by 32 publications

(26 citation statements)

References 73 publications

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“…3c). This finding is in keeping with recent evidence from a sensitive Next Generation Sequencing methodology (Strand-seq) that SCE occurs with a rate of 0.26 events/division in yeast 30 . Strand-seq experiments of normal human fibroblasts and lymphoblasts indicate the SCEs occur with a rate of 5 events/cell division 31 .…”

Section: Discussionsupporting

confidence: 90%

Rate volatility and asymmetric segregation diversify mutation burden in mutator cells

Dowsett

Sneeden

Olson

et al. 2020

Preprint

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Mutations that compromise mismatch repair (MMR) or DNA polymerase exonuclease 11domains produce mutator phenotypes capable of fueling cancer evolution. Tandem 12 defects in these pathways dramatically increase mutation rate. Here, we model how 13 mutator phenotypes expand genetic heterogeneity in budding yeast cells using a single-14 cell resolution approach that tallies all replication errors arising from individual 15divisions. The distribution of count data from cells lacking MMR and polymerase 16 proofreading was broader than expected for a single rate, consistent with volatility of the 17 mutator phenotype. The number of mismatches that segregated to the mother and 18 daughter cells after the initial round of replication co-varied, suggesting that 19 mutagenesis in each division is governed by a different underlying rate. The distribution 20 of "fixed" mutation counts that cells inherit is further broadened by an unequal sharing 21 of mutations due to semiconservative replication and Mendelian segregation. Modeling 22suggests that this asymmetric segregation may diversify mutation burden in mutator-23 driven tumors. 24 25

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Section: Discussionsupporting

confidence: 90%

Rate volatility and asymmetric segregation diversify mutation burden in mutator cells

Dowsett

Sneeden

Olson

et al. 2020

Preprint

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“…This difference can be leveraged to differentiate interactions between and within sister chromatids.BrdU containing DNA strands can be selectively degraded after Hoechst treatment and radiation with UV 3,12 . This property has been used before in strand-seq, which allows the detection of sister chromatid exchange events [13][14][15] . Here we describe SisterC, a method that combines Hi-C 16,17 on BrdU incorporated DNA and UV/Hoechst treatment to distinguish interactions between sister chromatids (inter-sister interactions) and along sister chromatids (intra-sister interactions).…”

mentioning

confidence: 99%

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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“…The interpretation of strand-specific binned read counts relies on the knowledge of the underlying state of template strands for a given chromosome (WW, CC, or WC). These "ground states" stay constant over the length of each chromosome in each single cell, unless they are altered through SCEs 21,71 . To detect SCEs, we performed the same segmentation procedure described above in each cell separately (as opposed to jointly across all cells, as for the segmentation).…”

Section: Discovery Of Deletions Duplications Inversions and Invertementioning

confidence: 99%

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes

Sanders¹,

Meiers²,

Ghareghani

et al. 2019

Preprint

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Structural variation (SV), where rearrangements delete, duplicate, invert or translocate DNA segments, is a major source of somatic cell variation. It can arise in rapid bursts, mediate genetic heterogenity, and dysregulate cancer-related pathways. The challenge to systematically discover SVs in single cells remains unsolved, with copy-neutral and complex variants typically escaping detection. We developed single cell tri-channel-processing (scTRIP), a computational framework that jointly integrates read depth, template strand and haplotype phase to comprehensively discover SVs in single cells. We surveyed SV landscapes of 565 single cell genomes, including transformed epithelial cells and patient-derived leukemic samples, and discovered abundant SV classes including inversions, translocations and large-scale genomic rearrangements mediating oncogenic dysregulation. We dissected the 'molecular karyotype' of the leukemic samples and examined their clonal structure. Different from prior methods, scTRIP also enabled direct detection and discrimination of SV mutational processes in individual cells, including breakage-fusion-bridge cycles. scTRIP will facilitate studies of clonal evolution, genetic mosaicism and somatic SV formation, and could improve disease classification for precision medicine.

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Genome-wide mapping of sister chromatid exchange events in single yeast cells using Strand-seq

Cited by 32 publications

References 73 publications

Rate volatility and asymmetric segregation diversify mutation burden in mutator cells

Rate volatility and asymmetric segregation diversify mutation burden in mutator cells

Detecting chromatin interactions along and between sister chromatids with SisterC

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes

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