Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos

被引:2
|
作者
Syed, Sahla [1 ]
Duan, Yifei [1 ,2 ]
Lim, Bomyi [1 ]
机构
[1] Univ Penn, Dept Chem & Biomol Engn, Philadelphia, PA 19104 USA
[2] Univ Penn, Master Biotechnol Program, Philadelphia, PA USA
来源
ELIFE | 2023年 / 12卷
基金
美国国家卫生研究院;
关键词
transcription kinetics; live imaging; MS2-MCP; transcription factors; transcription bursting; hidden-markov model; Drosophila embryos; D; melanogaster; TRANSCRIPTION FACTORS; SNAIL; EXPRESSION; ENHANCER; MESODERM; DORSAL; TWIST; ESTABLISHMENT; PATTERNS; GENOME;
D O I
10.7554/eLife.85997
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
收藏
页数:19
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