ABSTRACT Alternative splicing is controlled by differential binding of trans -acting RNA binding proteins (RBPs) to cis -regulatory elements in intronic and exonic pre-mRNA regions 1-3 . How secondary structure in the pre-mRNA transcripts affects recognition by RBPs and determines alternative exon usage is poorly understood. The MALT1 paracaspase is a key component of signaling pathways that mediate innate and adaptive immune responses 4 . Alternative splicing of MALT1 exon7 is critical for controlling optimal T cell activation 5,6 . Here, we demonstrate that processing of the MALT1 pre-mRNA depends on RNA structural elements that shield the 5’ and 3’ splice sites of the alternatively spliced exon7. By combining biochemical analyses with chemical probing and NMR we show that the RBPs hnRNP U and hnRNP L bind competitively and with comparable affinities to identical stem-loop RNA structures flanking the 5’ and 3’ splice sites of MALT1 exon7. While hnRNP U stabilizes RNA stem-loop conformations that maintain exon7 skipping, hnRNP L unwinds these RNA elements to facilitate recruitment of the essential splicing factor U2AF2 to promote exon7 inclusion. Our data represent a paradigm for the control of splice site selection by differential RBP binding and modulation of pre-mRNA structure.

Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of MALT1