dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation.
BACKGROUND
MicroRNAs (miRNAs) regulate several biological processes through post-transcriptional gene silencing. The efficiency of binding of miRNAs to target transcripts depends on the sequence as well as intramolecular structure of the transcript. Single Nucleotide Polymorphisms (SNPs) can contribute to alterations in the structure of regions flanking them, thereby influencing the accessibility for miRNA binding.


METHODS
The entire human genome was analyzed for SNPs in and around predicted miRNA target sites. Polymorphisms within 200 nucleotides that could alter the intramolecular structure at the target site, thereby altering regulation were annotated. Collated information was ported in a MySQL database with a user-friendly interface accessible through the URL: (http://miracle.igib.res.in/dbSMR).


CONCLUSIONS
The database has a user-friendly interface where the information can be queried using either the gene name, microRNA name, polymorphism ID or transcript ID. Combination queries using 'AND' or 'OR' is also possible along with specifying the degree of change of intramolecular bonding with and without the polymorphism. Such a resource would enable researchers address questions like the role of regulatory SNPs in the 3' UTRs and population specific regulatory modulations in the context of microRNA targets.
GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology (CSIR), Delhi, India. mh.manoj@gmail.com
Manoj
M
Hariharan
Vinod
V
Scaria
Samir K
SK
Brahmachari
D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D015894:Genome, Human; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020641:Polymorphism, Single Nucleotide
D035683:MicroRNAs