Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12574-9. doi: 10.1073/pnas.1207185109. Epub 2012 Jul 17.
Several 400- to 800-kb murine chromosome domains switch from early to late replication during loss of pluripotency, accompanied by a stable form of gene silencing that is resistant to reprogramming. We found that, whereas enhanced nuclease accessibility correlated with early replication genome-wide, domains that switch replication timing during differentiation were exceptionally inaccessible even when early-replicating. Nonetheless, two domains studied in detail exhibited substantial changes in transcriptional activity and higher-order chromatin unfolding confined to the region of replication timing change. Chromosome conformation capture (4C) data revealed that in the unfolded state in embryonic stem cells, these domains interacted preferentially with the early-replicating chromatin compartment, rarely interacting even with flanking late-replicating domains, whereas after differentiation, these same domains preferentially associated with late-replicating chromatin, including flanking domains. In both configurations they retained local boundaries of self-interaction, supporting the replication domain model of replication-timing regulation. Our results reveal a principle of developmentally regulated, large-scale chromosome folding involving a subnuclear compartment switch of inaccessible chromatin. This unusual level of regulation may underlie resistance to reprogramming in replication-timing switch regions.
在失去多能性的过程中，几个 400 到 800kb 的鼠类染色体区域从早期复制转变为晚期复制，同时伴随着一种稳定的基因沉默形式，这种形式对重编程具有抗性。我们发现，尽管增强的核酸酶可及性与全基因组的早期复制相关，但在分化过程中复制时间发生转变的区域即使在早期复制时也特别难以接近。尽管如此，我们详细研究的两个区域表现出转录活性的显著变化，以及在复制时间变化区域内的高级染色质展开。染色体构象捕获（4C）数据显示，在胚胎干细胞的展开状态下，这些区域优先与早期复制的染色质区室相互作用，即使与侧翼的晚期复制区域也很少相互作用，而在分化后，这些相同的区域优先与晚期复制的染色质区室相互作用，包括侧翼区域。在这两种构象中，它们都保留了自身相互作用的局部边界，支持复制时间调控的复制域模型。我们的结果揭示了一种发育调控的大规模染色体折叠的原理，涉及到核内不可接近染色质的亚核区室转换。这种不寻常的调控水平可能是复制时间转换区域对重编程具有抗性的基础。
