Detecting chromatin interactions along and between sister chromatids with SisterC

Abstract

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...

Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome

“…The ability of conventional Hi-C to capture intra-chromosomal ( cis ) contacts is well established. However, its ability to reveal trans contacts between sister-chromatids remains limited given the difficulty to distinguish both homologous molecules without incorporation of modified bases ( 51 ). Since Topo IV is mainly known for its involvement in the removal of inter-chromosomal links (or catenanes), presumably between allelic (or near-allelic) loci, we sought to test whether the emergence of prominent Hi-C signals spanning throughout the parE ts contact map could result from trans contacts.…”

Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data

“…New methods of chromatin conformation capture constantly emerge, including novel single-cell techniques, such as scSPRITE [ 35 ]. Methods that distinguish contacts of sister chromatids for a population of cells, such as SisterC [ 34 ] and scsHi-C [ 36 ], are of particular interest. We believe that with the development of single-cell Hi-C versions of these methods, DPDchrom would be effectively used to reconstruct conformations of diploid nuclei and genomes containing several copies of chromosomes.…”

High-Resolution Whole-Genome Analysis of Sister-Chromatid Contacts

“…Thus, Hi-SC2 is perfectly suited to analyze the frequency of contacts between sister DNA copies emerging from a replication fork. As a comparison, 3C-derived techniques cannot be used to map interactions between positions separated by less than 1,500 bp (Lajoie et al, 2015;Mitter et al, 2020;Oomen et al, 2020).…”

“…However, the resolution limit of microscopy and the restricted number of genomic positions that can be simultaneously visualized hampered the analysis of the many different processes that can influence the cohesiveness of newly replicated DNA molecules. Two conformation capture (3C)-based techniques were recently developed to map sisterchromatid interactions over a whole genome (Mitter et al, 2020;Oomen et al, 2020). The 3C methodology consists in fixing the intracellular conformation adopted by the chromosomes with a crosslinking agent before fragmentation with a restriction enzyme.…”