Super-enhancers are clusters of enhancer elements that play critical roles in the maintenance of cell identity. Current investigations on super-enhancers are centered on the established ones in static cell types. How super-enhancers are established during cell differentiation remains obscure. Here, by developing an unbiased approach to systematically analyze the evolving landscape of super-enhancers during cell differentiation in multiple lineages, we discover a general trend where super-enhancers emerge through three distinct temporal patterns: conserved, temporally hierarchical, and de novo. The three types of super-enhancers differ further in association patterns in target gene expression, functional enrichment, and 3D chromatin organization, suggesting they may represent distinct structural and functional subtypes. Furthermore, we dissect the enhancer repertoire within temporally hierarchical super-enhancers, and find enhancers that emerge at early and late stages are enriched with distinct transcription factors, suggesting that the temporal order of establishment of elements within super-enhancers may be directed by underlying DNA sequence. CRISPR-mediated deletion of individual enhancers in differentiated cells shows that both the early- and late-emerged enhancers are indispensable for target gene expression, while in undifferentiated cells early enhancers are involved in the regulation of target genes. In summary, our analysis highlights the heterogeneity of the super-enhancer population and provides new insights to enhancer functions within super-enhancers.

中文翻译：

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绘制细胞分化过程中超级增强子的演变图谱


超级增强子是增强子元件簇，在维持细胞身份方面发挥着关键作用。目前对超级增强子的研究主要集中在静态细胞类型中已建立的超级增强子。细胞分化过程中超级增强子是如何建立的仍然不清楚。在这里，通过开发一种公正的方法来系统地分析多个谱系的细胞分化过程中超级增强子的演变景观，我们发现了一个总体趋势，即超级增强子通过三种不同的时间模式出现：保守的、时间分层的和从头的。这三种类型的超级增强子在靶基因表达、功能富集和 3D 染色质组织的关联模式方面存在进一步差异，表明它们可能代表不同的结构和功能亚型。此外，我们剖析了时间分层超级增强子内的增强子库，发现早期和晚期出现的增强子富含不同的转录因子，这表明超级增强子内元素建立的时间顺序可能是由底层DNA指导的顺序。 CRISPR介导的分化细胞中单个增强子的缺失表明，早期和晚期出现的增强子对于靶基因的表达都是不可或缺的，而在未分化细胞中，早期增强子参与靶基因的调节。总之，我们的分析强调了超级增强子群体的异质性，并为超级增强子内的增强子功能提供了新的见解。