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bioRxiv · 10.1101/2021.10.12.464102

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

Jones, A. N.·Grass, C.·Meininger, I.·Geerlof, A.·Klostermann, M.·Zarnack, K.·Krappmann, D.·Sattler, M.
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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.

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Jones, A. N., Grass, C., Meininger, I., Geerlof, A., Klostermann, M., Zarnack, K., Krappmann, D., Sattler, M.. 2021-10-12. Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of MALT1. https://doi.org/10.1101/2021.10.12.464102

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