RNAmotifs: Prediction of multivalent RNA motifs that control alternative splicing

Matteo Cereda, Uberto Pozzoli, Gregor Rot, Peter Juvan, Anthony Schweitzer, Tyson Clark, Jernej Ule

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

RNA-binding proteins (RBPs) regulate splicing according to position-dependent principles, which can be exploited for analysis of regulatory motifs. Here we present RNAmotifs, a method that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. We show that diverse RBPs share basic positional principles, but differ in their propensity to enhance or repress exon inclusion. We assess exons differentially spliced between brain and heart, identifying known and new regulatory motifs, and predict the expression pattern of RBPs that bind these motifs.

Original languageEnglish
Article numberR20
JournalGenome Biology
Volume15
Issue number1
DOIs
Publication statusPublished - 2014

Fingerprint

Nucleotide Motifs
RNA-binding proteins
RNA-Binding Proteins
alternative splicing
Alternative Splicing
exons
RNA
Exons
prediction
Protein Splicing
protein
Amino Acid Motifs
heart
brain
Brain
methodology

ASJC Scopus subject areas

  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

RNAmotifs : Prediction of multivalent RNA motifs that control alternative splicing. / Cereda, Matteo; Pozzoli, Uberto; Rot, Gregor; Juvan, Peter; Schweitzer, Anthony; Clark, Tyson; Ule, Jernej.

In: Genome Biology, Vol. 15, No. 1, R20, 2014.

Research output: Contribution to journalArticle

Cereda, Matteo ; Pozzoli, Uberto ; Rot, Gregor ; Juvan, Peter ; Schweitzer, Anthony ; Clark, Tyson ; Ule, Jernej. / RNAmotifs : Prediction of multivalent RNA motifs that control alternative splicing. In: Genome Biology. 2014 ; Vol. 15, No. 1.
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