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Nucleic Acids Res. 2016 Jul 8;44(W1):W333-8. doi: 10.1093/nar/gkw410. Epub 2016 May 12.

rMAPS: RNA map analysis and plotting server for alternative exon regulation.

Author information

1
Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA juw.park@louisville.edu.
2
Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA.
3
Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA.
4
Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA.
5
Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA yxing@ucla.edu.

Abstract

RNA-binding proteins (RBPs) play a critical role in the regulation of alternative splicing (AS), a prevalent mechanism for generating transcriptomic and proteomic diversity in eukaryotic cells. Studies have shown that AS can be regulated by RBPs in a binding-site-position dependent manner. Depending on where RBPs bind, splicing of an alternative exon can be enhanced or suppressed. Therefore, spatial analyses of RBP motifs and binding sites around alternative exons will help elucidate splicing regulation by RBPs. The development of high-throughput sequencing technologies has allowed transcriptome-wide analyses of AS and RBP-RNA interactions. Given a set of differentially regulated alternative exons obtained from RNA sequencing (RNA-seq) experiments, the rMAPS web server (http://rmaps.cecsresearch.org) performs motif analyses of RBPs in the vicinity of alternatively spliced exons and creates RNA maps that depict the spatial patterns of RBP motifs. Similarly, rMAPS can also perform spatial analyses of RBP-RNA binding sites identified by cross-linking immunoprecipitation sequencing (CLIP-seq) experiments. We anticipate rMAPS will be a useful tool for elucidating RBP regulation of alternative exon splicing using high-throughput sequencing data.

PMID:
27174931
PMCID:
PMC4987942
DOI:
10.1093/nar/gkw410
[Indexed for MEDLINE]
Free PMC Article

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