GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences
Rumen Kostadinov,Nishtha Malhotra,Manuel Viotti,Robert J. Shine,Lawrence D'Antonio,Paramjeet Singh Bagga +5 more
TLDR
The computational approach is applied to map putative Quadruplex forming GRSs within the transcribed regions of a large number of alternatively processed human and mouse gene sequences that were obtained as fully annotated entries from GenBank and RefSeq to build the GRSDB database, which provides a unique avenue for studying G-quadruplexes in the context of RNA processing sites.Abstract:
Guanine-rich nucleic acids are known to form highly stable G-quadruplex structures, also known as G-quartets. Recently, there has been a tremendous amount of interest in studying G-quadruplexes owing to the realization of their biological importance. G-rich sequences (GRSs) capable of forming G-quadruplexes are found in the vicinity of polyadenylation regions and are involved in regulating 3' end processing of mammalian pre-mRNAs. G-rich motifs are also known to play an important role in alternative, tissue-specific splicing by interacting with hnRNP H protein subfamily. Whether quadruplex structure directly plays a role in regulating RNA processing events requires further investigation. To date there has not been a comprehensive effort to study G-quadruplexes near RNA processing sites. We have applied a computational approach to map putative Quadruplex forming GRSs within the transcribed regions of a large number of alternatively processed human and mouse gene sequences that were obtained as fully annotated entries from GenBank and RefSeq. We have used the computed data to build the GRSDB database that provides a unique avenue for studying G-quadruplexes in the context of RNA processing sites. GRSDB website offers visual comparison of G-quadruplex distribution patterns among all the alternative RNA products of a gene with the help of dynamic graphics. At present, GRSDB contains data from 1310 human and mouse genes, of which 1188 are alternatively processed. It has a total of 379 223 predicted G-quadruplexes, of which 54 252 are near RNA processing sites. GRSDB is a good resource for researchers interested in investigating the functional relevance of G-quadruplexes, especially in the context of alternative RNA processing. It can be accessed at http://bioinformatics.ramapo.edu/grsdb/.read more
Citations
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Journal ArticleDOI
Quadruplex DNA: sequence, topology and structure
TL;DR: This survey focuses on the folding and structural features on quadruplexes formed from telomeric and non-telomeric DNA sequences, and examines fundamental aspects of topology and the emerging relationships with sequence.
Journal ArticleDOI
Human telomere, oncogenic promoter and 5′-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics
TL;DR: The review highlights recent solution NMR-based G-quadruplex structures formed by the four-repeat human telomere in K+ solution and the guanine-rich strands of c-myc, c-kit and variant bcl-2 oncogenic promoters, as well as a bimolecular G- quadruplex that targets HIV-1 integrase.
Journal ArticleDOI
QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences
TL;DR: A web-based server that predicts quadruplex forming G-rich sequences (QGRS) in nucleotide sequences and features interactive graphic representation of the data is developed, very useful for investigating the functional relevance of G-quadruplex structure, in particular its role in regulating the gene expression by alternative processing.
Journal ArticleDOI
5′-UTR RNA G-quadruplexes: translation regulation and targeting
TL;DR: This review features the progresses in the study of 5′-UTR RNA G-quadruplex-mediated translational control and discusses protein trans-acting factors that have been implicated and the evidence that such RNA motifs have potential as small molecule target.
Journal ArticleDOI
G-Quadruplexes: Targets in Anticancer Drug Design
TL;DR: A summary of published research that has set out to address the problem of selectivity of G‐quadruplexes and research methodologies that have been developed to study the binding of ligands to G‐ quadruplexes are provided.
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