Delayed DNA replication in haploid human embryonic stem cells
- Matthew M. Edwards1,
- Michael V. Zuccaro2,3,
- Ido Sagi4,5,
- Qiliang Ding1,
- Dan Vershkov4,
- Nissim Benvenisty4,
- Dieter Egli2,3 and
- Amnon Koren1
- 1Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA;
- 2Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA;
- 3Columbia University Stem Cell Initiative, New York, New York 10032, USA;
- 4The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
Abstract
Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X Chromosome in haploids, consistent with the lack of X-Chromosome inactivation. We also identified 21 autosomal regions that had delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also underreplicated in polyploid placental cells. The same delays were observed in female ESCs with two active X Chromosomes, suggesting that increased X-Chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.275953.121.
- Received June 30, 2021.
- Accepted October 20, 2021.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
