Biallelic non-productive enhancer-promoter interaction precedes imprinted expression of KcnK9 during mouse neural commitment [RNA-seq]. Biallelic non-productive enhancer-promoter interaction precedes imprinted expression of KcnK9 during mouse neural commitment [RNA-seq]

How constitutive allelic methylation at imprinting control regions (ICRs) interacts with other levels of regulation to drive timely parental allele-specific expression along large imprinted domains remains partially understood at most imprinted loci. To gain insight into the regulation of the Peg13-KcnK9 domain, an imprinted domain with important brain functions, during neural commitment, we performed a detailed integrative analysis of the epigenetic, transcriptomic and cis-spatial organisation in an allele-specific manner in a mouse stem cell-based model of corticogenesis that recapitulates the control of imprinted gene expression in the embryonic brain. We have evidence that despite an allelic higher order chromatin structure associated with the paternally CTCF-bound Peg13 ICR, enhancer-Kcnk9 promoter contacts can occur on both alleles, although they are only productive on the maternal allele. This observation challenges the canonical model in which CTCF binding isolates the enhancer and its target gene on either side, and suggests a more nuanced role for allelic CTCF binding at the ICR of this locus. Overall design: RNA-seq generated on ES and NP cells for B6 x JF1 and JF1 x B6 genetic backgrounds.

在绝大多数印记基因座中，印记调控区（imprinting control regions, ICRs）的组成型等位基因甲基化如何与其他调控层级相互作用，以驱动大型印记结构域内适时的亲本等位基因特异性表达，目前仍未被完全阐明。为阐明具有重要脑功能的印记结构域Peg13-Kcnk9在神经定向分化过程中的调控机制，我们采用可重现胚胎脑内印记基因表达调控过程的小鼠干细胞源性皮质发生模型，以等位基因特异性方式对表观基因组、转录组及顺式空间结构开展了系统性整合分析。我们的研究证据显示，尽管与父本CCCTC结合因子（CTCF）结合的Peg13 ICR存在等位基因特异性高级染色质结构，但增强子与Kcnk9启动子的染色质互作可发生于两个等位基因，不过仅在母本等位基因上具有转录活性。这一发现挑战了经典模型——该模型认为CTCF结合可将增强子与其靶基因分别隔离在两侧，并提示该基因座ICR处的等位基因CTCF结合发挥着更为精细的调控作用。实验整体设计：针对B6×JF1及JF1×B6两种遗传背景，分别在胚胎干细胞（embryonic stem cells, ES）与神经前体细胞（neural progenitor cells, NP）中开展RNA测序（RNA-seq）。