干扰素-β增强子的基因调控逻辑具有两种选择性部署的转录因子协同模式。

Gene regulatory logic of the interferon-β enhancer is characterized by two selectively deployed modes of transcription factor synergy.

作者信息

Schiffman Allison, Cheng Zhang, Ourthiague Diana, Hoffmann Alexander

机构信息

Signaling Systems Laboratory, Department of Microbiology, Immunology and Molecular Genetics, and the Institute for Quantitative and Computational Biosciences, University of California Los Angeles, CA 90095.

出版信息

Proc Natl Acad Sci U S A. 2025 Aug 19;122(33):e2502800122. doi: 10.1073/pnas.2502800122. Epub 2025 Aug 12.

Abstract

Type I interferon IFNβ is a key immune response cytokine, and when its expression is dysregulated, it causes disease. The regulation of IFNβ enhancer has been a touchpoint of mammalian gene control research since the discovery of functional synergy between two stimulus-responsive transcription factors (TFs), nuclear factor kappa B (NFκB) and interferon regulatory factors (IRF). However, subsequent gene knockout studies revealed that in some conditions either NFκB or IRF activation can be dispensable, leaving the precise regulatory logic of IFNβ transcription an open question. Here, we developed a series of quantitative enhancer states models of IFNβ expression control and evaluated them with stimulus-response data from TF knockouts. Of these, our analysis reveals that two modes of TF synergy account for the available data and neither is based on binding cooperativity. The first involves two adjacent IRF dimers, with a sigmoidal binding curve at the distal site rendering it ultrasensitive and restricting it to conditions of high IRF activity upon viral infection. The second is driven by the proximal site, which has high affinity and synergizes with NFκB to enable about half-maximal expression in response to bacterial exposure. Its accessibility is controlled by the competitive repressor p50:p50, which prevents basal IRF from binding, such that NFκB-only stimuli do not induce IFNβ expression and may allow for prior-exposure-dependent tuning. The model explains how the regulatory logic of the IFNβ enhancer ensures invariant IFNβ expression in response to viral exposure, while providing tunable, context-dependent expression in response to bacterial exposure.

摘要

I型干扰素IFNβ是一种关键的免疫反应细胞因子,当其表达失调时会引发疾病。自发现两种刺激反应性转录因子(TFs)——核因子κB(NFκB)和干扰素调节因子(IRF)之间的功能协同作用以来,IFNβ增强子的调控一直是哺乳动物基因控制研究的一个切入点。然而,随后的基因敲除研究表明,在某些情况下,NFκB或IRF的激活可能是不必要的,这使得IFNβ转录的确切调控逻辑成为一个悬而未决的问题。在这里,我们开发了一系列IFNβ表达控制的定量增强子状态模型,并用来自TF敲除的刺激-反应数据对它们进行了评估。在这些模型中,我们的分析表明,两种TF协同模式可以解释现有数据,且都不是基于结合协同性。第一种模式涉及两个相邻的IRF二聚体,远端位点的S形结合曲线使其具有超敏感性,并将其限制在病毒感染时IRF高活性的条件下。第二种模式由近端位点驱动,近端位点具有高亲和力,并与NFκB协同作用,以在细菌暴露时实现约半数最大表达。其可及性由竞争性阻遏物p50:p50控制,p50:p50可防止基础IRF结合,因此仅NFκB刺激不会诱导IFNβ表达,并且可能允许进行先前暴露依赖性调节。该模型解释了IFNβ增强子的调控逻辑如何确保在病毒暴露时IFNβ表达不变,同时在细菌暴露时提供可调节的、依赖于上下文的表达。

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