Abstract
Condensin complexes are essential for chromosome condensation and segregation in mitosis, while condensin dysfunction, among other pathways leading to chromosomal bridging in mitosis, may play a role in tumor genomic instability, including recently discovered chromotripsis. To characterize potential double-strand breaks specifically occurring in late anaphase, human chromosomes depleted of condensin were analyzed by γ-H2AX ChIP followed by high-throughput sequencing (ChIP-seq). In condensin-depleted cells, the nonrepeated parts of the genome were shown to contain distinct γ-H2AX enrichment zones 75% of which overlapped with known hemizygous deletions in cancers. Furthermore, some tandemly repeated DNA sequences, analyzed separately from the rest of the genome, showed significant γ-H2AX enrichment in condensin-depleted anaphases. The most commonly occurring targets of such enrichment included simple repeats, centromeric satellites, and rDNA. The two latter categories indicate that acrocentric human chromosomes are especially susceptible to breaks upon condensin deficiency. The genomic regions that are specifically destabilized upon condensin dysfunction may constitute a condensin-specific chromosome destabilization pattern.
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Acknowledgments
We would like to thank J. Boeke and H. Hao for their advice on Roche-Nimlegen arrays, H. Morse for the critical suggestions, M. Stratton and G. Bignell for the fragile site datasets, K. Shirahige for the cohesin ChIP-seq data, Z. Abdullaev and E. Pugacheva for their advice on data analysis.
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Communicated by Frank Uhlmann
Authors Alexander Samoshkin and Stanimir Dulev contributed equally to this work.
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ESM 2
γ-H2AX enrichment peaks for SMC2-depleted anaphase cells from ChIP-seq experiments in BED file format. Two illumina sequence datasets were generated for each experimental condition, and the results were combined for analysis. Peaks were generated by CisGenome software, with the following parameters: bin size 150 bp, minimum peak length 600 bp. (CSV 26 kb)
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Samoshkin, A., Dulev, S., Loukinov, D. et al. Condensin dysfunction in human cells induces nonrandom chromosomal breaks in anaphase, with distinct patterns for both unique and repeated genomic regions. Chromosoma 121, 191–199 (2012). https://doi.org/10.1007/s00412-011-0353-6
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DOI: https://doi.org/10.1007/s00412-011-0353-6