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A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences

Enhancers are DNA sequences composed of transcription factor binding sites that drive complex patterns of gene expression in space and time. Until recently, studying enhancers in their genomic context was technically challenging. Therefore, minimal enhancers, the shortest pieces of DNA that can driv...

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Autores principales: López-Rivera, Francheska, Foster Rhoades, Olivia K., Vincent, Ben J., Pym, Edward C. G., Bragdon, Meghan D. J., Estrada, Javier, DePace, Angela H., Wunderlich, Zeba
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7718739/
https://www.ncbi.nlm.nih.gov/pubmed/33037064
http://dx.doi.org/10.1534/g3.120.401777
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author López-Rivera, Francheska
Foster Rhoades, Olivia K.
Vincent, Ben J.
Pym, Edward C. G.
Bragdon, Meghan D. J.
Estrada, Javier
DePace, Angela H.
Wunderlich, Zeba
author_facet López-Rivera, Francheska
Foster Rhoades, Olivia K.
Vincent, Ben J.
Pym, Edward C. G.
Bragdon, Meghan D. J.
Estrada, Javier
DePace, Angela H.
Wunderlich, Zeba
author_sort López-Rivera, Francheska
collection PubMed
description Enhancers are DNA sequences composed of transcription factor binding sites that drive complex patterns of gene expression in space and time. Until recently, studying enhancers in their genomic context was technically challenging. Therefore, minimal enhancers, the shortest pieces of DNA that can drive an expression pattern that resembles a gene’s endogenous pattern, are often used to study features of enhancer function. However, evidence suggests that some enhancers require sequences outside the minimal enhancer to maintain function under environmental perturbations. We hypothesized that these additional sequences also prevent misexpression caused by a transcription factor binding site mutation within a minimal enhancer. Using the Drosophila melanogaster even-skipped stripe 2 enhancer as a case study, we tested the effect of a Giant binding site mutation (gt-2) on the expression patterns driven by minimal and extended enhancer reporter constructs. We found that, in contrast to the misexpression caused by the gt-2 binding site deletion in the minimal enhancer, the same gt-2 binding site deletion in the extended enhancer did not have an effect on expression. The buffering of expression levels, but not expression pattern, is partially explained by an additional Giant binding site outside the minimal enhancer. Deleting the gt-2 binding site in the endogenous locus had no significant effect on stripe 2 expression. Our results indicate that rules derived from mutating enhancer reporter constructs may not represent what occurs in the endogenous context.
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spelling pubmed-77187392020-12-17 A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences López-Rivera, Francheska Foster Rhoades, Olivia K. Vincent, Ben J. Pym, Edward C. G. Bragdon, Meghan D. J. Estrada, Javier DePace, Angela H. Wunderlich, Zeba G3 (Bethesda) Investigations Enhancers are DNA sequences composed of transcription factor binding sites that drive complex patterns of gene expression in space and time. Until recently, studying enhancers in their genomic context was technically challenging. Therefore, minimal enhancers, the shortest pieces of DNA that can drive an expression pattern that resembles a gene’s endogenous pattern, are often used to study features of enhancer function. However, evidence suggests that some enhancers require sequences outside the minimal enhancer to maintain function under environmental perturbations. We hypothesized that these additional sequences also prevent misexpression caused by a transcription factor binding site mutation within a minimal enhancer. Using the Drosophila melanogaster even-skipped stripe 2 enhancer as a case study, we tested the effect of a Giant binding site mutation (gt-2) on the expression patterns driven by minimal and extended enhancer reporter constructs. We found that, in contrast to the misexpression caused by the gt-2 binding site deletion in the minimal enhancer, the same gt-2 binding site deletion in the extended enhancer did not have an effect on expression. The buffering of expression levels, but not expression pattern, is partially explained by an additional Giant binding site outside the minimal enhancer. Deleting the gt-2 binding site in the endogenous locus had no significant effect on stripe 2 expression. Our results indicate that rules derived from mutating enhancer reporter constructs may not represent what occurs in the endogenous context. Genetics Society of America 2020-10-09 /pmc/articles/PMC7718739/ /pubmed/33037064 http://dx.doi.org/10.1534/g3.120.401777 Text en Copyright © 2020 López-Rivera et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigations
López-Rivera, Francheska
Foster Rhoades, Olivia K.
Vincent, Ben J.
Pym, Edward C. G.
Bragdon, Meghan D. J.
Estrada, Javier
DePace, Angela H.
Wunderlich, Zeba
A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences
title A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences
title_full A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences
title_fullStr A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences
title_full_unstemmed A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences
title_short A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences
title_sort mutation in the drosophila melanogaster eve stripe 2 minimal enhancer is buffered by flanking sequences
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7718739/
https://www.ncbi.nlm.nih.gov/pubmed/33037064
http://dx.doi.org/10.1534/g3.120.401777
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