Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brains from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we showed that imprinted chromatin structure precedes imprinted expression at the locus. Additionally, activation of a distal enhancer induced imprinted expression of Kcnk9 in an allelic chromatin structure-dependent manner. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.

中文翻译：

---

神经发生过程中等位基因染色质结构先于 Kcnk9 的印记表达

从亲本配子继承的染色质状态的差异影响后代母本和父本等位基因的调节。这种现象被称为基因组印记，导致基因优先从一个亲本等位基因转录。虽然已知 DNA 甲基化等局部表观遗传因素对于印记基因表达的建立非常重要，但对于差异甲基化区域 (DMR) 导致广泛染色质等位基因表达差异的机制知之甚少。在多个印记位点观察到等位基因特异性高阶染色质结构，与在多个 DMR 处观察到的染色质组织因子 CTCF 的等位基因结合一致。然而，对于大多数印记位点，等位基因染色质结构是否影响等位基因表达尚不清楚。在这里，我们描述了Peg13-Kcnk9基因座（一个与智力障碍相关的印记区域）大脑特异性印记表达的机制。我们对来自相互杂交杂交的小鼠大脑进行了 Hi-C 区域捕获，发现了由 CTCF 与Peg13 DMR 等位基因结合引起的印记高阶染色质结构。使用体外神经元分化系统，我们发现印记染色质结构先于该位点的印记表达。此外，远端增强子的激活以等位基因染色质结构依赖性方式诱导Kcnk9的印记表达。这项工作提供了印记染色质结构的高分辨率图谱，并证明了早期发育中建立的染色质状态可以促进分化时的印记表达。