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

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. 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. Alternative splicing of MALT1 exon7 is critical for controlling optimal T cell activation. 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.

hucMSCs treatment prevents pulmonary fibrosis by reducing circANKRD42-YAP1-mediated mechanical stiffness

“…Further exploration was conducted on the circANKRD42 regulatory mechanism of hucMSCs treatment. Heterogeneous nuclear ribonucleoprotein L (hnRNP L) is an alternative RNA splicing factor involved in RNA splicing biogenesis [21]. Immunofluorescence images depicted that hnRNP L was located in the nucleus with or without hucMSCs/TGF-β1 treatment.…”

Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis

“…Recent studies have also shown the involvement of HNRNPU in mitosis and cell division by changing its interactions with condensed chromatin and influencing DNA replication and sister chromatid separation (Connolly et al, 2022; Ma et al, 2011; Sharp et al, 2020). Several studies have reported a role for HNRNPU in splicing, promoting both exon inclusion and exclusion (Huelga et al, 2012; Jones et al, 2022; Ye et al, 2015). Mechanistically, it has been shown that HNRNPU can stabilize the pre-mRNA structure, thus inhibiting the splicing of certain exons (Jones et al, 2022).…”

“…Several studies have reported a role for HNRNPU in splicing, promoting both exon inclusion and exclusion (Huelga et al, 2012; Jones et al, 2022; Ye et al, 2015). Mechanistically, it has been shown that HNRNPU can stabilize the pre-mRNA structure, thus inhibiting the splicing of certain exons (Jones et al, 2022). A critical role for Hnrnpu mediated splicing has also been demonstrated during pre- and postnatal heart development in mice, showing that loss of Hnrnpu leads to increased intron retention events, causing abnormality in heart development and function (Ye et al, 2015).…”