Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7

Abstract

HnRNP A1 regulates many alternative splicing events by the recognition of splicing silencer elements. Here, we provide the solution structures of its two RNA recognition motifs (RRMs) in complex with short RNA. In addition, we show by NMR that both RRMs of hnRNP A1 can bind simultaneously to a single bipartite motif of the human intronic splicing silencer ISS-N1, which controls survival of motor neuron exon 7 splicing. RRM2 binds to the upstream motif and RRM1 to the downstream motif. Combining the insights from the structure with in cell splicing assays we show that the architecture and organization of the two RRMs is essential to hnRNP A1 function. The disruption of the inter-RRM interaction or the loss of RNA binding capacity of either RRM impairs splicing repression by hnRNP A1. Furthermore, both binding sites within the ISS-N1 are important for splicing repression and their contributions are cumulative rather than synergistic.DOI: http://dx.doi.org/10.7554/eLife.25736.001

Crystal and solution structures of human oncoprotein Musashi‐2 N‐terminal RNA recognition motif 1

“…For example, the NMR structure of HNRNP A1 RRM1 (PDB ID: 2LYV; RMSD for 70 Cα‐atoms: 1.16 Å), the crystal structure of HNRNP A1 RRM1(PDB ID: 1UP1; RMSD for 73 Cα‐atoms: 1.11 Å), the NMR structure of CYP33 RRM (PDB ID: 2KYX; RMSD for 61 Cα‐atoms: 1.16 Å), the NMR structure of Hu antigen C RBD1 (PDB ID: 1D8Z; RMSD for 61 Cα‐atoms: 1.47 Å), the crystal structure of hnRNP A18 RRM (PDB ID: 5TBX; RMSD for 66 Cα‐atoms: 1.39 Å), and the NMR structure of drosophila sex‐lethal RBD1 (PDB ID: 2SXL; RMSD for 61 Cα‐atoms: 1.61 Å). Interestingly, the NMR structures of both apo and RNA bound form of HNRNP A1 RRM1 (PDB ID 2LYV and 5MPG) are similar to the NMR structure of MSI2‐RRM1 in that the β2/β3 loop and Arg 55 (corresponding to Arg 62 in MSI2‐RRM1) of the apo HNRNP A1 RRM1 adopts the RNA bound conformation (Figure B).…”

Mechanism of Splicing Regulation of Spinal Muscular Atrophy Genes

“…The location of this site right next to the other hnRNP A1-binding site created by the C6U mutation within exon 7 strikingly resembles the arrangement of two putative hnRNP A1 sites within ISS-N1. As recently proposed, close proximity of the two hnRNP A1 sites is conducive for a tight interaction involving two RRMs of a single hnRNP A1 molecule [95]. The polypyrimidine tract (PPT) at the 3′ ss of exon 7 has been suggested to harbor a positive element associated with hnRNP C (Fig.…”

“…3; [52]). This model has been recently revised to suggest that two RNA-recognition motifs (RRMs) of a single hnRNP A1 molecule interact with two putative sites within ISS-N1 [95]. Noticeably, the cytosine residue at the first position (10C) of ISS-N1 does not fall within the putative hnRNP A1/A2-binding site.…”

Impact of RNA–Protein Interaction Modes on Translation Control: The Versatile Multidomain Protein Gemin5

“…In addition to canonical RBDs, various RBPs contain low‐complexity motifs, such as RGG, and regions intrinsically unstructured mediating RNA and protein contacts. Examples of these proteins are members of the stress granules, including the glycine‐tryptophan protein of 182 kDa; proteins causing repeat‐associated degenerative diseases, such as the fragile X mental retardation protein or C9ORF72; and factors controlling splicing, transport, and other steps of the RNA lifespan, like the transactive response DNA‐binding protein 43 (TDP‐43) or hnRNPA1 . Intrinsically unstructured regions could behave as flexible linkers connecting RBDs, allowing a dynamic conformation of RNP complexes, a key aspect in the regulation of gene expression .…”