Login Register Cart 0
Generic placeholder image

Current Bioinformatics

Editor-in-Chief

ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Research Article

ZFARED: A Database of the Antioxidant Response Elements in Zebrafish

Author(s): Azhwar Raghunath, Raju Nagarajan and Ekambaram Perumal*

Volume 15, Issue 5, 2020

Page: [415 - 419] Pages: 5

DOI: 10.2174/1574893614666191018172213

Price: $65

Abstract

Background: Antioxidant Response Elements (ARE) play a key role in the expression of Nrf2 target genes by regulating the Keap1-Nrf2-ARE pathway, which offers protection against toxic agents and oxidative stress-induced diseases.

Objective: To develop a database of putative AREs for all the genes in the zebrafish genome. This database will be helpful for researchers to investigate Nrf2 regulatory mechanisms in detail.

Methods: To facilitate researchers functionally characterize zebrafish AREs, we have developed a database of AREs, Zebrafish Antioxidant Response Element Database (ZFARED), for all the protein-coding genes including antioxidant and mitochondrial genes in the zebrafish genome. The front end of the database was developed using HTML, JavaScript, and CSS and tested in different browsers. The back end of the database was developed using Perl scripts and Perl-CGI and Perl- DBI modules.

Results: ZFARED is the first database on the AREs in zebrafish, which facilitates fast and efficient searching of AREs. AREs were identified using the in-house developed Perl algorithms and the database was developed using HTML, JavaScript, and Perl-CGI scripts. From this database, researchers can access the AREs based on chromosome number (1 to 25 and M for mitochondria), strand (positive or negative), ARE pattern and keywords. Users can also specify the size of the upstream/promoter regions (5 to 30 kb) from transcription start site to access the AREs located in those specific regions.

Conclusion: ZFARED will be useful in the investigation of the Keap1-Nrf2-ARE pathway and its gene regulation. ZFARED is freely available at http://zfared.buc.edu.in/.

Keywords: Antioxidant response elements, database, Keap1-Nrf2-ARE pathway, Nrf2, ZFARED, zebrafish.

« Previous Next »
Graphical Abstract

[1]
Lieschke GJ, Currie PD. Animal models of human disease: zebrafish swim into view. Nat Rev Genet 2007; 8(5): 353-67.
[http://dx.doi.org/10.1038/nrg2091] [PMID: 17440532]
[2]
Nowik N, Podlasz P, Jakimiuk A, Kasica N, Sienkiewicz W, Kaleczyc J. Zebrafish: an animal model for research in veterinary medicine. Pol J Vet Sci 2015; 18(3): 663-74.
[http://dx.doi.org/10.1515/pjvs-2015-0086] [PMID: 26618602]
[3]
Fuse Y, Kobayashi M. Conservation of the Keap1-Nrf2 system. An evolutionary journey through stressful space and time. Molecules 2017; 22(3) E436
[http://dx.doi.org/10.3390/molecules22030436] [PMID: 28282941]
[4]
Hahn ME, Timme-Laragy AR, Karchner SI, Stegeman JJ. Nrf2 and Nrf2-related proteins in development and developmental toxicity: Insights from studies in zebrafish (Danio rerio). Free Radic Biol Med 2015; 88(Pt B): 275-89.
[5]
Raghunath A, Sundarraj K, Nagarajan R, et al. Antioxidant response elements: Discovery, classes, regulation and potential applications. Redox Biol 2018; 17: 297-314.
[http://dx.doi.org/10.1016/j.redox.2018.05.002] [PMID: 29775961]
[6]
Suzuki T, Takagi Y, Osanai H, et al. Pi class glutathione S-transferase genes are regulated by Nrf 2 through an evolutionarily conserved regulatory element in zebrafish. Biochem J 2005; 388(Pt 1): 65-73.
[http://dx.doi.org/10.1042/BJ20041860] [PMID: 15654768]
[7]
Timme-Laragy AR, Karchner SI, Franks DG, et al. Nrf2b, novel zebrafish paralog of oxidant-responsive transcription factor NF-E2-related factor 2 (NRF2). J Biol Chem 2012; 287(7): 4609-27.
[http://dx.doi.org/10.1074/jbc.M111.260125] [PMID: 22174413]
[8]
Rousseau ME, Sant KE, Borden LR, Franks DG, Hahn ME, Timme-Laragy AR. Regulation of Ahr signaling by Nrf2 during development: Effects of Nrf2a deficiency on PCB126 embryotoxicity in zebrafish (Danio rerio). Aquat Toxicol 2015; 167: 157-71.
[http://dx.doi.org/10.1016/j.aquatox.2015.08.002] [PMID: 26325326]
[9]
Raghunath A, Nagarajan R, Sundarraj K, Panneerselvam L, Perumal E. Genome-wide identification and analysis of Nrf2 binding sites - Antioxidant response elements in zebrafish. Toxicol Appl Pharmacol 2018; 360: 236-48.
[http://dx.doi.org/10.1016/j.taap.2018.09.013] [PMID: 30243843]
[10]
Zheng Y, Li X, Hu H. PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples. Database (Oxford) 2015; 2015 pii bav007
[http://dx.doi.org/10.1093/database/bav007]
[11]
Lapatas V, Stefanidakis M, Jimenez RC, Via A, Schneider MV. Data integration in biological research: an overview. J Biol Res (Thessalon) 2015; 22(1): 9.
[http://dx.doi.org/10.1186/s40709-015-0032-5] [PMID: 26336651]
[12]
Palsson B. The challenges of in silico biology. Nat Biotechnol 2000; 18(11): 1147-50.
[http://dx.doi.org/10.1038/81125] [PMID: 11062431]
[13]
Chervitz SA, Deutsch EW, Field D, et al. Data standards for Omics data: the basis of data sharing and reuse. Methods Mol Biol 2011; 719: 31-69.
[http://dx.doi.org/10.1007/978-1-61779-027-0_2] [PMID: 21370078]
[14]
Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol 2015; 50(6): 550-73.
[http://dx.doi.org/10.3109/10409238.2015.1087961] [PMID: 26446758]
[15]
Dodson M, de la Vega MR, Cholanians AB, Schmidlin CJ, Chapman E, Zhang DD. Modulating NRF2 in disease: Timing is everything. Annu Rev Pharmacol Toxicol 2019; 59: 555-75.
[http://dx.doi.org/10.1146/annurev-pharmtox-010818-021856] [PMID: 30256716]

Rights & Permissions Print Cite
Article Metrics
9
© 2024 Bentham Science Publishers | Privacy Policy