Cereda Matteo, Pozzoli Uberto, Rot Gregor, Juvan Peter, Schweitzer Anthony, Clark Tyson, Ule Jernej
Genome Biol. 2014 Jan 31;15(1):R20. doi: 10.1186/gb-2014-15-1-r20.
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.
RNA结合蛋白（RBPs）根据位置依赖性原则调控剪接，这一特性可用于分析调控基序。在此，我们介绍RNAmotifs，这是一种评估差异调控的可变外显子周围序列，以识别短序列和简并序列簇（称为多价RNA基序）的方法。我们表明，不同的RBPs共享基本的位置原则，但在增强或抑制外显子包含的倾向方面存在差异。我们评估了大脑和心脏之间差异剪接的外显子，识别出已知和新的调控基序，并预测了结合这些基序的RBPs的表达模式。RNAmotifs可在https://bitbucket.org/rogrro/rna_motifs获取。
