Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [ATAC-seq]

Genomic imprinting is an epigenetic phenomenon in which genes exhibit restricted or biased expression from one allele according to parental origin. Imprinted gene expression plays a crucial role in the development, including the brain. Higher-order chromatin structure has long been associated with gene regulation, particularly in the context of spatial enhancer-promoter interactions. Given the characteristic parental allele-biased expression pattern of imprinted genes, a compelling question is whether the three-dimensional organization of parental genomes plays a role in imprinted gene regulation. Using a capture Hi-C approach, we identifiedparental allele-specific higher-order chromatin structures across multiple imprinted domains in the mouse brain. These allele-specific structural features largely stem from annotated imprinting control regions (ICRs), concomitant with allele-specific binding of CTCF. Detailed analysis suggests that transcriptional start sites (TSS) of active and inactive alleles of imprinted genes form distinct chromatin interactions, differing in degree and/or type. CRISPRi screeningrevealed a distal cis-regulatory element that modulates imprinted expression of the Mest-Copg2locus in neurons, and its regulatory mechanism is tightly associated with allele-specific chromatin interactions. Further investigation revealed that both a cis-acting long non-coding RNA and allele-specific enhancer-promoter architecture modulates Mest-Copg2 imprinted expression. Together, this study highlights the interplay between chromatin structure and regulatory landscapes that modulate allele-specific expression of imprinted genes. Overall design: ATAC-seq datasets from 8-weeks-old mouse cortices, including forward (BxC) and reverse (CxB) crosses.

基因组印记（Genomic imprinting）是一种表观遗传现象，指基因按照亲本来源仅从单个等位基因表现出受限或偏倚的表达模式。印记基因的表达在包括大脑在内的生物体发育过程中发挥关键作用。长期以来，高级染色质结构（higher-order chromatin structure）与基因调控密切相关，尤其在空间增强子-启动子相互作用的研究背景下。鉴于印记基因具有亲本等位基因偏倚表达的典型特征，一个引人关注的问题是：亲本基因组的三维组织结构是否参与印记基因的调控过程。本研究采用捕获Hi-C（capture Hi-C）技术，在小鼠大脑的多个印记结构域中鉴定出亲本等位基因特异性的高级染色质结构。这些等位基因特异性结构特征主要源自已注释的印记控制区（ICRs），并伴随CTCF的等位基因特异性结合。详细分析显示，印记基因活跃与非活跃等位基因的转录起始位点（TSS）形成了不同的染色质相互作用模式，二者在作用程度和/或类型上存在差异。CRISPR干扰筛选（CRISPRi screening）结果表明，存在一个远端顺式调控元件，可调控神经元中Mest-Copg2基因座的印记表达，其调控机制与等位基因特异性染色质相互作用紧密相关。进一步研究发现，顺式作用长链非编码RNA（cis-acting long non-coding RNA）与等位基因特异性增强子-启动子架构共同调控Mest-Copg2的印记表达。综上，本研究揭示了染色质结构与调控网络之间的相互作用，该相互作用可调控印记基因的等位基因特异性表达。实验整体设计：取自8周龄小鼠大脑皮层的ATAC测序（ATAC-seq）数据集，包含正交（BxC）与反交（CxB）两种交配组合。