Cell-to-cell heterogeneity is a characteristic feature of the tumor necrosis factor (TNF)-stimulated inflammatory response mediated by the transcription factor NF-κB, motivating an exploration of the underlying sources of this noise. Here we combined single-transcript measurements with computational models to study transcriptional noise at six NF-κB-regulated inflammatory genes. In the basal state, NF-κB-target genes displayed an inverse correlation between mean and noise. TNF stimulation increased transcription while maintaining noise, except for the most repressed genes. By fitting transcript distributions to a two-state model of promoter activity, we found that TNF primarily stimulated transcription by increasing burst size while maintaining burst frequency. Burst size increases were associated with enrichment of initiated-but-paused RNA polymerase II at the promoter, and blocking the release of paused RNAPII with a small molecule inhibitor decreased TNF-stimulated burst size. Finally, we used a mathematical model to show that TNF positive feedback further amplified gene expression noise resulting from burst-size mediated transcription, leading to diverse TNF functional outputs. Our results reveal potential sources of noise underlying intercellular heterogeneity in the TNF- mediated inflammatory response.

中文翻译：

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TNF刺激主要调节NF-κB调控基因的转录爆发大小

细胞间异质性是由转录因子NF-κB介导的肿瘤坏死因子（TNF）刺激的炎症反应的特征，促使人们探索这种噪声的潜在来源。在这里，我们将单转录本测量与计算模型相结合，以研究六个NF-κB调节的炎症基因的转录噪声。在基础状态下，NF-κB-靶基因在均值和噪声之间呈反比关系。TNF刺激可增加转录，同时保持噪音，但最受压抑的基因除外。通过使转录物分布适合启动子活性的两个状态模型，我们发现TNF主要通过增加猝发大小同时维持猝发频率来刺激转录。爆发大小的增加与启动子上起始但暂停的RNA聚合酶II的富集有关，并且用小分子抑制剂阻止暂停的RNAPII的释放会降低TNF刺激的爆发大小。最后，我们使用数学模型显示TNF阳性反馈进一步放大了由突发大小介导的转录产生的基因表达噪声，从而导致了多种TNF功能输出。我们的研究结果揭示了在TNF介导的炎症反应中潜在的细胞间异质性噪声的潜在来源。导致多种TNF功能输出。我们的研究结果揭示了在TNF介导的炎症反应中潜在的细胞间异质性噪声的潜在来源。导致多种TNF功能输出。我们的研究结果揭示了在TNF介导的炎症反应中潜在的细胞间异质性噪声的潜在来源。