Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos.
Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos.
复制标题
蛋白质-DNA 结合的调节揭示了早期果蝇胚胎中时空基因控制的机制。
DOI：
10.1101/2023.01.05.522923
复制
发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Lim,Bomyi
中科院分区：
文献类型：
--
作者：
Syed,Sahla;Duan,Yifei;Lim,Bomyi
众所周知，增强子通过将转录因子（tf）招募到该区域的同源结合位点来调节其靶基因的时空表达。然而，相同tf的多个结合位点及其特定的空间排列在决定增强子整体能力中的作用尚未完全了解。在本研究中，我们利用MS2-MCP实时成像技术定量分析了蜗牛远端增强子在早期果蝇胚胎中的调控逻辑。通过系统调节该增强子中的Dorsal和Twist结合基序，我们发现这些结合位点中的任何一个突变都会导致转录幅度的急剧减少，从而导致靶基因mRNA的产生减少。我们提供了协同作用的证据，例如具有中等亲和力的多个结合位点合作招募更多的tf来驱动比单个位点更强的转录活性。此外，基于隐马尔可夫的随机转录模型显示，结合位点突变的胚胎更有可能回到非活性启动子状态。我们提出TF-DNA结合调节空间和时间基因表达，并通过调节转录动力学和调节爆发率来驱动强大的模式形成。
It is well known that enhancers regulate the spatiotemporal expression of their target genes by recruiting transcription factors (TFs) to the cognate binding sites in the region. However, the role of multiple binding sites for the same TFs and their specific spatial arrangement in determining the overall competency of the enhancer has yet to be fully understood. In this study, we utilized the MS2-MCP live imaging technique to quantitatively analyze the regulatory logic of the snail distal enhancer in early Drosophila embryos. Through systematic modulation of Dorsal and Twist binding motifs in this enhancer, we found that a mutation in any one of these binding sites causes a drastic reduction in transcriptional amplitude, resulting in a reduction in mRNA production of the target gene. We provide evidence of synergy, such that multiple binding sites with moderate affinities cooperatively recruit more TFs to drive stronger transcriptional activity than a single site. Moreover, a Hidden Markov-based stochastic model of transcription reveals that embryos with mutated binding sites have a higher probability of returning to the inactive promoter state. We propose that TF-DNA binding regulates spatial and temporal gene expression and drives robust pattern formation by modulating transcriptional kinetics and tuning bursting rates.