Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology and Center for Biosystems Dynamics Research, Kobe, Japan.
Laboratory of Molecular & Cellular Biology, Graduate Schoold of Bioresources, Mie University, Tsu, Japan.
Nat Genet. 2019 Sep;51(9):1356-1368. doi: 10.1038/s41588-019-0474-z. Epub 2019 Aug 12.
In mammalian cells, chromosomes are partitioned into megabase-sized topologically associating domains (TADs). TADs can be in either A (active) or B (inactive) subnuclear compartments, which exhibit early and late replication timing (RT), respectively. Here, we show that A/B compartments change coordinately with RT changes genome wide during mouse embryonic stem cell (mESC) differentiation. While A to B compartment changes and early to late RT changes were temporally inseparable, B to A changes clearly preceded late to early RT changes and transcriptional activation. Compartments changed primarily by boundary shifting, altering the compartmentalization of TADs facing the A/B compartment interface, which was conserved during reprogramming and confirmed in individual cells by single-cell Repli-seq. Differentiating mESCs altered single-cell Repli-seq profiles gradually but uniformly, transiently resembling RT profiles of epiblast-derived stem cells (EpiSCs), suggesting that A/B compartments might also change gradually but uniformly toward a primed pluripotent state. These results provide insights into how megabase-scale chromosome organization changes in individual cells during differentiation.
在哺乳动物细胞中，染色体被分割成兆碱基大小的拓扑关联域（TAD）。TAD 可以处于 A（活跃）或 B（非活跃）亚核区室中，分别表现出早期和晚期复制时间（RT）。在这里，我们表明，在小鼠胚胎干细胞（mESC）分化过程中，A/B 区室与 RT 变化在整个基因组范围内协调变化。虽然 A 到 B 区室的变化和早期到晚期 RT 的变化在时间上是不可分割的，但 B 到 A 的变化明显先于晚期到早期 RT 的变化和转录激活。区室的变化主要通过边界移动来实现，改变了面临 A/B 区室界面的 TAD 的区室化，这在重编程过程中是保守的，并通过单细胞 Repli-seq 在单个细胞中得到证实。分化的 mESC 逐渐但均匀地改变了单细胞 Repli-seq 图谱，短暂地类似于外胚层来源的干细胞（EpiSCs）的 RT 图谱，这表明 A/B 区室也可能逐渐但均匀地向启动的多能状态转变。这些结果为我们提供了在单个细胞分化过程中，兆碱基级染色体组织如何变化的见解。
