Several thousand sex-differential distal enhancers have been identified in mouse liver; however, their links to sex-biased genes and the impact of any sex-differences in nuclear organization and chromatin interactions are unknown. To address these issues, we first characterized 1847 mouse liver genomic regions showing significant sex differential occupancy by cohesin and CTCF, two key 3D nuclear organizing factors. These sex-differential binding sites were primarily distal to sex-biased genes but rarely generated sex-differential TAD (topologically associating domain) or intra-TAD loop anchors, and were sometimes found in TADs without sex-biased genes. A substantial subset of sex-biased cohesin-non-CTCF binding sites, but not sex-biased cohesin-and-CTCF binding sites, overlapped sex-biased enhancers. Cohesin depletion reduced the expression of male-biased genes with distal, but not proximal, sex-biased enhancers by >10-fold, implicating cohesin in long-range enhancer interactions regulating sex-biased genes. Using circularized chromosome conformation capture-based sequencing (4C-seq), we showed that sex differences in distal sex-biased enhancer–promoter interactions are common. Intra-TAD loops with sex-independent cohesin-and-CTCF anchors conferred sex specificity to chromatin interactions indirectly, by insulating sex-biased enhancer–promoter contacts and by bringing sex-biased genes into closer proximity to sex-biased enhancers. Furthermore, sex-differential chromatin interactions involving sex-biased gene promoters, enhancers, and lncRNAs were associated with sex-biased binding of cohesin and/or CTCF. These studies elucidate how 3D genome organization impacts sex-biased gene expression in a non-reproductive tissue through both direct and indirect effects of cohesin and CTCF looping on distal enhancer interactions with sex-differentially expressed genes.

中文翻译：

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由粘连蛋白和 CTCF 环引导的 3D 基因组组织对小鼠肝脏中性别偏向的染色质相互作用和基因表达的影响。


在小鼠肝脏中已鉴定出数千个性别差异远端增强子；然而，它们与性别偏见基因的联系以及核组织和染色质相互作用中性别差异的影响尚不清楚。为了解决这些问题，我们首先对 1847 个小鼠肝脏基因组区域进行了表征，这些区域显示粘连蛋白和 CTCF（两个关键的 3D 核组织因子）占据的显着性别差异。这些性别差异结合位点主要位于性别偏向基因的远端，但很少产生性别差异 TAD（拓扑关联域）或 TAD 内环锚，有时在没有性别偏向基因的 TAD 中发现。性别偏见的粘连蛋白-非 CTCF 结合位点的一个重要子集，而不是性别偏见的粘连蛋白-和 CTCF 结合位点，与性别偏见的增强子重叠。粘连蛋白耗尽使具有远端而非近端性别偏向增强子的雄性偏向基因的表达降低了>10倍，这表明粘连蛋白参与了调节性别偏向基因的远程增强子相互作用。使用基于环化染色体构象捕获的测序（4C-seq），我们发现远端性别偏向的增强子-启动子相互作用中的性别差异很常见。具有性别无关的粘连蛋白和 CTCF 锚的 TAD 内环通过隔离性别偏向的增强子-启动子接触以及使性别偏向的基因更接近性别偏向的增强子，间接赋予染色质相互作用性别特异性。此外，涉及性别偏向基因启动子、增强子和lncRNA的性别差异染色质相互作用与粘连蛋白和/或CTCF的性别偏向结合相关。 这些研究阐明了 3D 基因组组织如何通过粘连蛋白和 CTCF 环对远端增强子与性别差异表达基因相互作用的直接和间接影响，影响非生殖组织中的性别偏向基因表达。