QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes

Abstract

Emerging evidence indicates the importance of G-quadruplex motifs as drug targets. [Stuart A. Borman, Ascent of quadruplexes-nucleic acid structures become promising drug targets. Chem. Eng. News, 2007;85, 12-17], which stems from the fact that these motifs are present in a surprising number of promoters wherein their role in controlling gene expression has been demonstrated for a few. We present a compendium of quadruplex motifs, with particular focus on their occurrence and conservation in promoters-QuadBase. It is composed of two parts (EuQuad and ProQuad). EuQuad gives information on quadruplex motifs present within 10 kb of transcription starts sites in 99 980 human, chimpanzee, rat and mouse genes. ProQuad contains quadruplex information of 146 prokaryotes. Apart from gene-specific searches for quadruplex motifs, QuadBase has a number of other modules. 'Orthologs Analysis' queries for conserved motifs across species based on a selected reference organism; 'Pattern Search' can be used to fetch specific motifs of interest from a selected organism using user-defined criteria for quadruplex motifs, i.e. stem, loop size, etc. 'Pattern Finder' tool can search for motifs in any given sequence. QuadBase is freely available to users from non-profit organization at http://quadbase.igib.res.in/.

Figure 1.

Schematic representation of G4 motif. Red planes show three G-tetrads constituting the stem (left panel) and hydrogen bonding scheme of guanines forming tetrad is shown in right panel.

Figure 2.

Database architecture for EuQuad and ProQuad. Relational database containing PG4 motif information of human, rat, mouse, chimpanzee and 146 prokaryotes. In Pattern Search, organism is selected with other query parameters such as pattern type, stem size, genomic location and loop size. Orthologs Analysis retrieves information based on query fired for selected genes of selected reference organism. All output is in html as well as in downloadable format.

Figure 3.

Graphical representation of conserved PG4 motif within promoters. Searched motifs that are conserved in rat, mouse and chimpanzee with human as reference organism are shown. Each horizontal line represents promoter sequence (4 kb centered at TSS). Color boxes represent total PG4 motifs in promoter sequence and width represents relative length of the motif. Yellow boxes represent conserved G4 motifs with respect to the one selected.