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/.
A distinct class of antioxidant response elements is consistently activated in tumors with NRF2 mutations