QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences

Abstract

The quadruplex structures formed by guanine-rich nucleic acid sequences have received significant attention recently because of growing evidence for their role in important biological processes and as therapeutic targets. G-quadruplex DNA has been suggested to regulate DNA replication and may control cellular proliferation. Sequences capable of forming G-quadruplexes in the RNA have been shown to play significant roles in regulation of polyadenylation and splicing events in mammalian transcripts. Whether quadruplex structure directly plays a role in regulating RNA processing requires investigation. Computational approaches to study G-quadruplexes allow detailed analysis of mammalian genomes. There are no known easily accessible user-friendly tools that can compute G-quadruplexes in the nucleotide sequences. We have developed a web-based server, QGRS Mapper, that predicts quadruplex forming G-rich sequences (QGRS) in nucleotide sequences. It is a user-friendly application that provides many options for defining and studying G-quadruplexes. It performs analysis of the user provided genomic sequences, e.g. promoter and telomeric regions, as well as RNA sequences. It is also useful for predicting G-quadruplex structures in oligonucleotides. The program provides options to search and retrieve desired gene/nucleotide sequence entries from NCBI databases for mapping G-quadruplexes in the context of RNA processing sites. This feature is very useful for investigating the functional relevance of G-quadruplex structure, in particular its role in regulating the gene expression by alternative processing. In addition to providing data on composition and locations of QGRS relative to the processing sites in the pre-mRNA sequence, QGRS Mapper features interactive graphic representation of the data. The user can also use the graphics module to visualize QGRS distribution patterns among all the alternative RNA products of a gene simultaneously on a single screen. QGRS Mapper can be accessed at http://bioinformatics.ramapo.edu/QGRS/.

Figure 1

QGRS Mapper Analysis Page. This page allows the user to enter a nucleotide sequence or to search NCBI for a nucleotide entry that will then be analyzed for the presence of QGRS. The user may enter the sequence in raw or FASTA format or search NCBI by Gene ID, Gene name or Accession number. There are options to define the QGRS for the search, including: the maximum length, the minimum number of guanine tetrads, loop length and composition.

Figure 2

GREB1—Gene View. The first table in this view gives a summary of the gene being analyzed. This includes information such as the gene ID, name, symbol, a link to the corresponding NCBI entry, and the number of alternatively processed products and poly(A) signals found in the gene. The total number of QGRS in the gene is given for both non-overlapping and overlapping sequences. For each product, the numbers of exons and introns that were analyzed are given, together with the number of QGRS. Also, an exon/intron map is given. For the entire gene or for a particular product the user may select from three buttons to obtain more detailed information about the QGRS in the gene. These buttons are labeled Data View, Data View (with overlaps) and Graphics View. Only one product is shown in the figure. The screenshot showing all products can be found in the Supplementary Data.

Figure 3

GREB1—Data View. A table of gene information is given at the top of the figure. The second table lists all QGRS mapped to exons and introns of the product, including information about the position of the QGRS, its distance from 3′ and 5′ splice sites, the actual sequence (underlining the G-groups) and its G-score.

Figure 4

GREB1—Graphics View. A graphic representation of the gene, a sliding window that shows a fragment of the gene, and a graph showing the location and G-score for the non-overlapping QGRS in that fragment. A tool is provided to let the user zoom in or out on any portion of the gene. The nucleotide sequence is visible at maximum zoom levels.