Super-enhancers (SEs) govern the expression of genes defining cell identity. However, the dynamic landscape of SEs and their critical constituent enhancers involved in skeletal muscle development remains unclear. In this study, using pig as a model, we employed CUT&Tag to profile the enhancer-associated histone modification marker H3K27ac in skeletal muscle across two prenatal and three postnatal stages and investigated how SEs influence skeletal muscle development. We identified three SE families with distinct temporal dynamics: continuous (Con, 397), transient (TS, 434), and de novo (DN, 756). These SE families are associated with different temporal gene expression trajectories, biological functions, and DNA methylation levels. Notably, several lines of evidence suggest a potential prominent role of Con SEs in regulating porcine muscle development and meat traits. To pinpoint key cis-regulatory units in Con SEs, we developed an integrative approach that leverages information from eRNA annotation, GWAS signals and high-throughput capture STARR-seq experiments. Within Con SEs, we identified 20 candidate critical enhancers with meat and carcass-associated DNA variations that affect enhancer activity and inferred their upstream TFs and downstream target genes. As a proof of concept, we experimentally validated the role of one such enhancer and its potential target gene during myogenesis. Our findings reveal the dynamic regulatory features of SEs in skeletal muscle development and provide a general integrative framework for identifying critical enhancers underlying the formation of complex traits.

中文翻译：

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分析超级增强子的时间动力学揭示了骨骼肌发育的潜在关键增强子及其基因调控网络


超级增强子 （SE） 控制定义细胞身份的基因的表达。然而，参与骨骼肌发育的 SEs 及其关键组成增强子的动态景观仍不清楚。在这项研究中，以猪为模型，我们采用 CUT&Tag 来剖析 2 个产前和 3 个产后阶段骨骼肌中增强子相关的组蛋白修饰标志物 H3K27ac，并研究 SEs 如何影响骨骼肌发育。我们确定了三个具有不同时间动态的 SE 家族：连续 （Con， 397）、瞬态 （TS， 434） 和从头 （DN， 756）。这些 SE 家族与不同的时间基因表达轨迹、生物学功能和 DNA 甲基化水平有关。值得注意的是，几条证据表明 Con SEs 在调节猪肌肉发育和肉类性状方面具有潜在的突出作用。为了确定 Con SE 中的关键顺式调节单元，我们开发了一种综合方法，该方法利用来自 eRNA 注释、GWAS 信号和高通量捕获 STARR-seq 实验的信息。在 Con SEs 中，我们确定了 20 个候选关键增强子，这些增强子具有影响增强子活性的肉类和胴体相关 DNA 变异，并推断了它们的上游 TFs 和下游靶基因。作为概念验证，我们实验验证了一种此类增强子及其潜在靶基因在肌发生过程中的作用。我们的研究结果揭示了 SEs 在骨骼肌发育中的动态调节特征，并为识别复杂特征形成的关键增强子提供了一个通用的综合框架。