CpG islands (CGIs) represent a distinctive and widespread genetic feature of vertebrate genomes, being associated with ~70% of all annotated gene promoters. CGIs have been proposed to control transcription initiation by conferring nearby promoters with unique chromatin properties. In addition, there are thousands of distal or orphan CGIs (oCGIs) whose functional relevance and mechanism of action are barely known. Here we show that oCGIs are an essential component of poised enhancers (PEs) that boost their long-range regulatory activity and dictate the responsiveness of their target genes. Using a CRISPR/Cas9 knock-in strategy in mESC, we introduced PEs with or without oCGIs within topological associating domains (TADs) harbouring genes with different types of promoters. By evaluating the chromatin, topological and regulatory properties of the engineered PEs, we uncover that, rather than increasing their local activation, oCGIs boost the physical and functional communication between PEs and distally located developmental genes. Furthermore, we demonstrate that developmental genes with CpG rich promoters are particularly responsive to PEs and that such responsiveness depends on the presence of oCGIs. Therefore, our work unveils a novel role for CGIs as genetic determinants of the compatibility between genes and enhancers, thus providing major insights into how developmental gene expression programs are deployed under both physiological and pathological conditions.

中文翻译：

---

孤儿CpG孤岛可增强平衡增强子的调节活性，并决定其靶基因的响应能力

CpG岛（CGI）代表了脊椎动物基因组的独特而广泛的遗传特征，与所有带注释的基因启动子的70％相关。已经提出了通过赋予附近具有独特染色质特性的启动子来控制转录起始的CGI。此外，还有数千个远端或孤儿CGI（oCGI），其功能相关性和作用机制鲜为人知。在这里，我们表明oCGI是平衡增强子（PE）的重要组成部分，增强了它们的长期调节活性并决定了其靶基因的响应能力。在mESC中使用CRISPR / Cas9敲入策略，我们引入了带有或不带有oCGI的PE，它们在拓扑关联域（TAD）中包含具有不同类型启动子的基因。通过评估染色质，工程PE的拓扑和调节特性，我们发现oCGI并没有增加其局部激活，反而促进了PE与位于远端的发育基因之间的物理和功能交流。此外，我们证明具有丰富CpG启动子的发育基因对PE尤其有反应，而这种反应取决于oCGI的存在。因此，我们的工作揭示了CGI作为基因和增强子之间相容性的遗传决定因素的新颖作用，从而为在生理和病理条件下如何部署发育基因表达程序提供了重要见识。此外，我们证明具有丰富CpG启动子的发育基因对PE尤其敏感，而这种响应性取决于oCGI的存在。因此，我们的工作揭示了CGI作为基因和增强子之间相容性的遗传决定因素的新颖作用，从而为在生理和病理条件下如何部署发育基因表达程序提供了重要见识。此外，我们证明具有丰富CpG启动子的发育基因对PE尤其有反应，而这种反应取决于oCGI的存在。因此，我们的工作揭示了CGI作为基因和增强子之间相容性的遗传决定因素的新颖作用，从而为在生理和病理条件下如何部署发育基因表达程序提供了重要见识。