Genome-wide stability of the DNA replication program in single mammalian cells
Genome-wide stability of the DNA replication program in single mammalian cells
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DOI：
10.1038/s41588-019-0347-5
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发表时间：
2017-12
期刊：
影响因子：
30.8
通讯作者：
Saori Takahashi;Hisashi Miura;Takahiro Shibata;Koji Nagao;K. Okumura;Masato Ogata;C. Obuse;S. Takebayashi;I. Hiratani
中科院分区：
文献类型：
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作者：
Saori Takahashi;Hisashi Miura;Takahiro Shibata;Koji Nagao;K. Okumura;Masato Ogata;C. Obuse;S. Takebayashi;I. Hiratani
在这里，我们报告了一种单细胞DNA复制测序方法，scd-seq，一种全基因组方法，可以测量复制和未复制DNA之间的拷贝数差异。使用scd-seq，我们证明了复制结构域组织在单个小鼠胚胎干细胞（mESC）中是保守的。分化的mESC表现出不同的配置文件，这也是保守的细胞之间。单倍型解析的scd-seq揭示了同源常染色体的相似复制谱，而失活的X染色体明显比其活性对应物晚复制。然而，细胞与细胞之间的复制时间的异质性是存在的，这是最小的开始和结束的S期。此外，发育调节域被发现偏离他人，并表现出更高程度的异质性，从而表明与发育可塑性的联系。此外，等位基因表达失衡被发现与复制定时不平衡密切相关。我们的结果为单细胞水平了解DNA复制调节奠定了基础，并提供了对三维基因组组织的见解。
Here, we report a single-cell DNA replication sequencing method, scRepli-seq, a genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication-domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct profiles, which were also conserved among cells. Haplotype-resolved scRepli-seq revealed similar replication profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication-timing heterogeneity was present, which was smallest at the beginning and the end of S phase. In addition, developmentally regulated domains were found to deviate from others and showed a higher degree of heterogeneity, thus suggesting a link to developmental plasticity. Moreover, allelic expression imbalance was found to strongly associate with replication-timing asynchrony. Our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into three-dimensional genome organization.