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

Behura SK, Sarro J, Li P, Mysore K, Severson DW, Emrich SJ, Duman-Scheel M - BMC Genomics (2016)

Bottom Line: 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.All of the elements tested in vivo were confirmed to drive gene expression in transgenic Drosophila reporter assays.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.

View Article: PubMed Central - PubMed

Affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

FPs upstream of non-coding A. aegypti genes. tRNA, rRNA, snRNA, and microRNAs have FPs within 1 kb upstream of their TSSs
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Fig6: FPs upstream of non-coding A. aegypti genes. tRNA, rRNA, snRNA, and microRNAs have FPs within 1 kb upstream of their TSSs

Mentions: Major classes of A. aegypti non-coding genes including tRNA, rRNA, snRNA, and microRNAs, also have FPs within 1 kb upstream of their TSSs (Fig. 6; Additional file 10). The precursor transcripts of miRNA genes are known to be regulated by cis-acting elements [46, 47], thus suggesting that FPs identified within 1 kb upstream of 43 A. aegypti miRNA genes may play a significant role in regulating synthesis of their precursors. Similarly, specific sequences upstream of tRNA genes are also known to regulate synthesis of tRNA molecules [48]. 287 FPs are associated with upstream sequences within 1 kb of ~30 % of A. aegypti tRNA genes, indicating possible cis-regulation of isoacceptor tRNAs. In addition to miRNA and tRNA, snRNA and rRNA genes have also been found to have association with cis-acting regulators [49, 50], and FPs were found to flank these genes in A. aegypti.Fig. 6


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

Behura SK, Sarro J, Li P, Mysore K, Severson DW, Emrich SJ, Duman-Scheel M - BMC Genomics (2016)

FPs upstream of non-coding A. aegypti genes. tRNA, rRNA, snRNA, and microRNAs have FPs within 1 kb upstream of their TSSs
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4862039&req=5

Fig6: FPs upstream of non-coding A. aegypti genes. tRNA, rRNA, snRNA, and microRNAs have FPs within 1 kb upstream of their TSSs
Mentions: Major classes of A. aegypti non-coding genes including tRNA, rRNA, snRNA, and microRNAs, also have FPs within 1 kb upstream of their TSSs (Fig. 6; Additional file 10). The precursor transcripts of miRNA genes are known to be regulated by cis-acting elements [46, 47], thus suggesting that FPs identified within 1 kb upstream of 43 A. aegypti miRNA genes may play a significant role in regulating synthesis of their precursors. Similarly, specific sequences upstream of tRNA genes are also known to regulate synthesis of tRNA molecules [48]. 287 FPs are associated with upstream sequences within 1 kb of ~30 % of A. aegypti tRNA genes, indicating possible cis-regulation of isoacceptor tRNAs. In addition to miRNA and tRNA, snRNA and rRNA genes have also been found to have association with cis-acting regulators [49, 50], and FPs were found to flank these genes in A. aegypti.Fig. 6

Bottom Line: 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.All of the elements tested in vivo were confirmed to drive gene expression in transgenic Drosophila reporter assays.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.

View Article: PubMed Central - PubMed

Affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus