Tjalsma Sjoerd J D, Rinzema Niels J, Verstegen Marjon J A M, Robers Michelle J, Nieto-Aliseda Andrea, Gremmen Richard A, Allahyar Amin, Muraro Mauro J, Krijger Peter H L, de Laat Wouter
Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
Single Cell Discoveries, Utrecht, the Netherlands.
Cell Genom. 2025 Mar 12;5(3):100778. doi: 10.1016/j.xgen.2025.100778. Epub 2025 Feb 25.
Cell-type-specific gene activation is regulated by enhancers, sometimes located at large genomic distances from target gene promoters. Whether distal enhancers require specific factors to orchestrate gene regulation remains unclear. Here, we used enhancer distance-controlled reporter screens to find candidate factors. We depleted them and employed activity-by-contact predictions to genome-wide classify genes based on enhancer distance. Predicted distal enhancers typically control tissue-restricted genes and often are strong enhancers. We find cohesin, but also mediator, most specifically required for long-range activation, with cohesin repressing short-range gene activation and prioritizing distal over proximal HBB genes competing for shared enhancers. Long-range controlled genes are also most sensitive to perturbations of other regulatory proteins and to BET inhibitor JQ1, this being more a consequence of their distinct enhancer features than distance. Our work predicts that lengthening of intervening sequences can help limit the expression of target genes to specialized cells with optimal trans-factor environments.
细胞类型特异性基因激活受增强子调控，这些增强子有时位于与靶基因启动子距离很远的基因组区域。远端增强子是否需要特定因子来协调基因调控仍不清楚。在这里，我们利用增强子距离控制的报告基因筛选来寻找候选因子。我们将它们耗尽，并采用基于接触的活性预测对全基因组的基因根据增强子距离进行分类。预测的远端增强子通常控制组织特异性基因，并且往往是强增强子。我们发现黏连蛋白以及中介体对于远距离激活最为关键，黏连蛋白抑制近距离基因激活，并在竞争共享增强子的情况下优先选择远端HBB基因而非近端HBB基因。远距离控制的基因对其他调节蛋白的扰动以及BET抑制剂JQ1也最为敏感，这更多是由于它们独特的增强子特征而非距离所致。我们的研究预测，中间序列的延长有助于将靶基因的表达限制在具有最佳转录因子环境的特化细胞中。
