Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology; RNA Therapeutics Institute
Amino Acids, Peptides, and Proteins | Biological Phenomena, Cell Phenomena, and Immunity | Genetic Phenomena | Genomics | Investigative Techniques | Structural Biology | Systems Biology
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 S-phase, 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.
Genomics, chromatin, SisterC, chromosome conformation capture assay, chromatids
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The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
DOI of Published Version
bioRxiv 2020.03.10.986208; doi: https://doi.org/10.1101/2020.03.10.986208. Link to preprint on bioRxiv service.
Oomen ME, Hedger AK, Watts JK, Dekker J. (2020). Detecting chromatin interactions along and between sister chromatids with SisterC [preprint]. University of Massachusetts Medical School Faculty Publications. https://doi.org/10.1101/2020.03.10.986208. Retrieved from https://escholarship.umassmed.edu/faculty_pubs/1669
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