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High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti

BACKGROUND: Despite substantial progress in mosquito genomic and genetic research, few cis-regulatory elements (CREs), DNA sequences that control gene expression, have been identified in mosquitoes or other non-model insects. Formaldehyde-assisted isolation of regulatory elements paired with DNA seq...

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Autores principales: Behura, Susanta K., Sarro, Joseph, Li, Ping, Mysore, Keshava, Severson, David W., Emrich, Scott J., Duman-Scheel, Molly
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862039/
https://www.ncbi.nlm.nih.gov/pubmed/27161480
http://dx.doi.org/10.1186/s12864-016-2468-x
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author Behura, Susanta K.
Sarro, Joseph
Li, Ping
Mysore, Keshava
Severson, David W.
Emrich, Scott J.
Duman-Scheel, Molly
author_facet Behura, Susanta K.
Sarro, Joseph
Li, Ping
Mysore, Keshava
Severson, David W.
Emrich, Scott J.
Duman-Scheel, Molly
author_sort Behura, Susanta K.
collection PubMed
description BACKGROUND: Despite substantial progress in mosquito genomic and genetic research, few cis-regulatory elements (CREs), DNA sequences that control gene expression, have been identified in mosquitoes or other non-model insects. Formaldehyde-assisted isolation of regulatory elements paired with DNA sequencing, FAIRE-seq, is emerging as a powerful new high-throughput tool for global CRE discovery. FAIRE results in the preferential recovery of open chromatin DNA fragments that are not bound by nucleosomes, an evolutionarily conserved indicator of regulatory activity, which are then sequenced. Despite the power of the approach, FAIRE-seq has not yet been applied to the study of non-model insects. In this investigation, we utilized FAIRE-seq to profile open chromatin and identify likely regulatory elements throughout the genome of the human disease vector mosquito Aedes aegypti. We then assessed genetic variation in the regulatory elements of dengue virus susceptible (Moyo-S) and refractory (Moyo-R) mosquito strains. RESULTS: Analysis of sequence data obtained through next generation sequencing of FAIRE DNA isolated from A. aegypti embryos revealed >121,000 FAIRE peaks (FPs), many of which clustered in the 1 kb 5’ upstream flanking regions of genes known to be expressed at this stage. As expected, known transcription factor consensus binding sites were enriched in the FPs, and of these FoxA1, Hunchback, Gfi, Klf4, MYB/ph3 and Sox9 are most predominant. All of the elements tested in vivo were confirmed to drive gene expression in transgenic Drosophila reporter assays. Of the >13,000 single nucleotide polymorphisms (SNPs) recently identified in dengue virus-susceptible and refractory mosquito strains, 3365 were found to map to FPs. CONCLUSION: FAIRE-seq analysis of open chromatin in A. aegypti permitted genome-wide discovery of CREs. The results of this investigation indicate that FAIRE-seq is a powerful tool for identification of regulatory DNA in the genomes of non-model organisms, including human disease vector mosquitoes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2468-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-48620392016-05-11 High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti Behura, Susanta K. Sarro, Joseph Li, Ping Mysore, Keshava Severson, David W. Emrich, Scott J. Duman-Scheel, Molly BMC Genomics Research Article BACKGROUND: Despite substantial progress in mosquito genomic and genetic research, few cis-regulatory elements (CREs), DNA sequences that control gene expression, have been identified in mosquitoes or other non-model insects. Formaldehyde-assisted isolation of regulatory elements paired with DNA sequencing, FAIRE-seq, is emerging as a powerful new high-throughput tool for global CRE discovery. FAIRE results in the preferential recovery of open chromatin DNA fragments that are not bound by nucleosomes, an evolutionarily conserved indicator of regulatory activity, which are then sequenced. Despite the power of the approach, FAIRE-seq has not yet been applied to the study of non-model insects. In this investigation, we utilized FAIRE-seq to profile open chromatin and identify likely regulatory elements throughout the genome of the human disease vector mosquito Aedes aegypti. We then assessed genetic variation in the regulatory elements of dengue virus susceptible (Moyo-S) and refractory (Moyo-R) mosquito strains. RESULTS: Analysis of sequence data obtained through next generation sequencing of FAIRE DNA isolated from A. aegypti embryos revealed >121,000 FAIRE peaks (FPs), many of which clustered in the 1 kb 5’ upstream flanking regions of genes known to be expressed at this stage. As expected, known transcription factor consensus binding sites were enriched in the FPs, and of these FoxA1, Hunchback, Gfi, Klf4, MYB/ph3 and Sox9 are most predominant. All of the elements tested in vivo were confirmed to drive gene expression in transgenic Drosophila reporter assays. Of the >13,000 single nucleotide polymorphisms (SNPs) recently identified in dengue virus-susceptible and refractory mosquito strains, 3365 were found to map to FPs. CONCLUSION: FAIRE-seq analysis of open chromatin in A. aegypti permitted genome-wide discovery of CREs. The results of this investigation indicate that FAIRE-seq is a powerful tool for identification of regulatory DNA in the genomes of non-model organisms, including human disease vector mosquitoes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2468-x) contains supplementary material, which is available to authorized users. BioMed Central 2016-05-10 /pmc/articles/PMC4862039/ /pubmed/27161480 http://dx.doi.org/10.1186/s12864-016-2468-x Text en © Behura et al. 2016 Open AccessThis article is 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 you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Behura, Susanta K.
Sarro, Joseph
Li, Ping
Mysore, Keshava
Severson, David W.
Emrich, Scott J.
Duman-Scheel, Molly
High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti
title High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti
title_full High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti
title_fullStr High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti
title_full_unstemmed High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti
title_short High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti
title_sort high-throughput cis-regulatory element discovery in the vector mosquito aedes aegypti
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862039/
https://www.ncbi.nlm.nih.gov/pubmed/27161480
http://dx.doi.org/10.1186/s12864-016-2468-x
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