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Regeneration and Developmental Enhancers Are Differentially Compatible with Minimal Promoters

Ian J. Begeman, Benjamin Emery, Andrew Kurth, View ORCID ProfileJunsu Kang
doi: https://doi.org/10.1101/2022.06.20.496839
Ian J. Begeman
1Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI, 53705, USA.
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Benjamin Emery
1Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI, 53705, USA.
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Andrew Kurth
1Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI, 53705, USA.
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Junsu Kang
1Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI, 53705, USA.
2UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin– Madison, Madison, WI, 53705, USA
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  • ORCID record for Junsu Kang
  • For correspondence: junsu.kang@wisc.edu
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ABSTRACT

Enhancers and promoters are cis-regulatory elements that control gene expression. Enhancers are activated in a cell type-, tissue-, and condition-specific manner to stimulate promoter function and transcription. Zebrafish have emerged as a powerful animal model for examining the activities of enhancers derived from various species through transgenic enhancer assays, in which an enhancer is coupled with a minimal promoter. However, the efficiency of minimal promoters and their compatibility with multiple developmental and regeneration enhancers have not been systematically tested in zebrafish. Thus, we assessed the efficiency of six minimal promoters and comprehensively interrogated the compatibility of the promoters with developmental and regeneration enhancers. We found that the fos minimal promoter and Drosophila synthetic core promoter (DSCP) yielded high rates of leaky expression that may complicate the interpretation of enhancer assays. Notably, the adenovirus E1b promoter, the zebrafish lepb 0.8-kb (P0.8) and lepb 2-kb (P2) promoters, and a new zebrafish synthetic promoter (ZSP) that combines elements of the E1b and P0.8 promoters drove little or no ectopic expression, making them suitable for transgenic assays. We also found significant differences in compatibility among specific combinations of promoters and enhancers, indicating the importance of promoters as key regulatory elements determining the specificity of gene expression. Our study provides guidelines for transgenic enhancer assays in zebrafish to aid in the discovery of functional enhancers regulating development and regeneration.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 20, 2022.
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Regeneration and Developmental Enhancers Are Differentially Compatible with Minimal Promoters
Ian J. Begeman, Benjamin Emery, Andrew Kurth, Junsu Kang
bioRxiv 2022.06.20.496839; doi: https://doi.org/10.1101/2022.06.20.496839
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Regeneration and Developmental Enhancers Are Differentially Compatible with Minimal Promoters
Ian J. Begeman, Benjamin Emery, Andrew Kurth, Junsu Kang
bioRxiv 2022.06.20.496839; doi: https://doi.org/10.1101/2022.06.20.496839

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