title: GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences.
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/.
authors.affiliation: Bioinformatics Group, School of Theoretical and Applied Science, Ramapo College of New Jersey, Mahwah, NJ 07430, USA.
authors.forename: Rumen
authors.initials: R
authors.lastname: Kostadinov
authors.forename: Nishtha
authors.initials: N
authors.lastname: Malhotra
authors.forename: Manuel
authors.initials: M
authors.lastname: Viotti
authors.forename: Robert
authors.initials: R
authors.lastname: Shine
authors.forename: Lawrence
authors.initials: L
authors.lastname: D'Antonio
authors.forename: Paramjeet
authors.initials: P
authors.lastname: Bagga
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D003196:Computer Graphics; D030561:Databases, Nucleic Acid; D006147:Guanine / Q000737:chemistry*; D006801:Humans; D020407:Internet; D051379:Mice; D026721:RNA 3' End Processing; D039104:RNA 3' Polyadenylation Signals; D012322:RNA Precursors / Q000737:chemistry*; D022821:RNA Splice Sites; D012333:RNA, Messenger / Q000737:chemistry*; D038621:Regulatory Sequences, Ribonucleic Acid; D014584:User-Computer Interface
chemical_list: D012322:RNA Precursors; D022821:RNA Splice Sites; D012333:RNA, Messenger; D038621:Regulatory Sequences, Ribonucleic Acid; D006147:Guanine