RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing.
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. RNAmotifs is available at https://bitbucket.org/rogrro/rna_motifs.
Matteo
M
Cereda
Uberto
U
Pozzoli
Gregor
G
Rot
Peter
P
Juvan
Anthony
A
Schweitzer
Tyson
T
Clark
Jernej
J
Ule
D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D001921:Brain / Q000166:cytology / Q000378:metabolism; D002460:Cell Line; D005091:Exons; D006321:Heart / Q000502:physiology; D006801:Humans; D051379:Mice; D018345:Mice, Knockout; D046228:Microarray Analysis; D059372:Nucleotide Motifs / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D016601:RNA-Binding Proteins