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

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 ov...

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Autores principales: Syed, Sahla, Duan, Yifei, Lim, Bomyi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10629816/
https://www.ncbi.nlm.nih.gov/pubmed/37934571
http://dx.doi.org/10.7554/eLife.85997
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author Syed, Sahla
Duan, Yifei
Lim, Bomyi
author_facet Syed, Sahla
Duan, Yifei
Lim, Bomyi
author_sort Syed, Sahla
collection PubMed
description 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.
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spelling pubmed-106298162023-11-08 Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos Syed, Sahla Duan, Yifei Lim, Bomyi eLife Chromosomes and Gene Expression 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. eLife Sciences Publications, Ltd 2023-11-07 /pmc/articles/PMC10629816/ /pubmed/37934571 http://dx.doi.org/10.7554/eLife.85997 Text en © 2023, Syed et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Chromosomes and Gene Expression
Syed, Sahla
Duan, Yifei
Lim, Bomyi
Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos
title Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos
title_full Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos
title_fullStr Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos
title_full_unstemmed Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos
title_short Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos
title_sort modulation of protein-dna binding reveals mechanisms of spatiotemporal gene control in early drosophila embryos
topic Chromosomes and Gene Expression
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10629816/
https://www.ncbi.nlm.nih.gov/pubmed/37934571
http://dx.doi.org/10.7554/eLife.85997
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AT limbomyi modulationofproteindnabindingrevealsmechanismsofspatiotemporalgenecontrolinearlydrosophilaembryos