scholarly journals Quantitative fine-tuning of photoreceptor cis-regulatory elements through affinity modulation of transcription factor binding sites

Gene Therapy ◽  
2010 ◽  
Vol 17 (11) ◽  
pp. 1390-1399 ◽  
Author(s):  
J Lee ◽  
C A Myers ◽  
N Williams ◽  
M Abdelaziz ◽  
J C Corbo
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Regulatory Elements ◽  
Transcription Factor Binding ◽  
Fine Tuning ◽  
Factor Binding ◽  
Affinity Modulation

scholarly journals Regulation of spatiotemporal limits of developmental gene expression via enhancer grammar

2020 ◽  
Vol 117 (26) ◽  
pp. 15096-15103 ◽  
Author(s):  
Samuel H. Keller ◽  
Siddhartha G. Jena ◽  
Yuji Yamazaki ◽  
Bomyi Lim
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Binding Site ◽  
Binding Sites ◽  
Transcriptional Activity ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Fine Tuning ◽  
Factor Binding

The regulatory specificity of a gene is determined by the structure of its enhancers, which contain multiple transcription factor binding sites. A unique combination of transcription factor binding sites in an enhancer determines the boundary of target gene expression, and their disruption often leads to developmental defects. Despite extensive characterization of binding motifs in an enhancer, it is still unclear how each binding site contributes to overall transcriptional activity. Using live imaging, quantitative analysis, and mathematical modeling, we measured the contribution of individual binding sites in transcriptional regulation. We show that binding site arrangement within the Rho-GTPase componentt48enhancer mediates the expression boundary by mainly regulating the timing of transcriptional activation along the dorsoventral axis ofDrosophilaembryos. By tuning the binding affinity of the Dorsal (Dl) and Zelda (Zld) sites, we show that single site modulations are sufficient to induce significant changes in transcription. Yet, no one site seems to have a dominant role; rather, multiple sites synergistically drive increases in transcriptional activity. Interestingly, Dl and Zld demonstrate distinct roles in transcriptional regulation. Dl site modulations change spatial boundaries oft48, mostly by affecting the timing of activation and bursting frequency rather than transcriptional amplitude or bursting duration. However, modulating the binding site for the pioneer factor Zld affects both the timing of activation and amplitude, suggesting that Zld may potentiate higher Dl recruitment to target DNAs. We propose that such fine-tuning of dynamic gene control via enhancer structure may play an important role in ensuring normal development.

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