STarMir Tools for Prediction of microRNA Binding Sites.
MicroRNAs (miRNAs) are a class of endogenous short noncoding RNAs that regulate gene expression by targeting messenger RNAs (mRNAs), which results in translational repression and/or mRNA degradation. As regulatory molecules, miRNAs are involved in many mammalian biological processes and also in the manifestation of certain human diseases. As miRNAs play central role in the regulation of gene expression, understanding miRNA-binding patterns is essential to gain an insight of miRNA mediated gene regulation and also holds promise for therapeutic applications. Computational prediction of miRNA binding sites on target mRNAs facilitates experimental investigation of miRNA functions. This chapter provides protocols for using the STarMir web server for improved predictions of miRNA binding sites on a target mRNA. As an application module of the Sfold RNA package, the current version of STarMir is an implementation of logistic prediction models developed with high-throughput miRNA binding data from cross-linking immunoprecipitation (CLIP) studies. The models incorporated comprehensive thermodynamic, structural, and sequence features, and were found to make improved predictions of both seed and seedless sites, in comparison to the established algorithms (Liu et al., Nucleic Acids Res 41:e138, 2013). Their broad applicability was indicated by their good performance in cross-species validation. STarMir is freely available at http://sfold.wadsworth.org/starmir.html .
Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY, 12208, USA.
Shaveta
S
Kanoria
Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY, 12208, USA.
William
W
Rennie
Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY, 12208, USA.
Chaochun
C
Liu
Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY, 12208, USA.
C Steven
CS
Carmack
Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT, 06520, USA.
Jun
J
Lu
Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY, 12208, USA. ye.ding@health.ny.gov.
Ye
Y
Ding
D020029:Base Pairing; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics; D009690:Nucleic Acid Conformation; D059370:RNA Folding; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
D035683:MicroRNAs; D012333:RNA, Messenger
CLIP; RNA secondary structure; Target mRNA; miRNA; miRNA binding site
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