Journal Article

Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43

Daujotyte, Dalia, Allain, Frédéric H-T, Lukavsky, Peter J, Damberger, Fred F, Tollervey, James R, Buratti, Emanuele, Stuani, Cristiana, Baralle, Francisco E, Ule, Jernej

2013

Overview

TDP-43 regulates alternative splicing of the cystic fibrosis transmembrane regulator (CFTR) and is found in cytosolic granules associated with several neurodegenerative disorders. A new solution structure of the tandem RNA-recognition motifs (RRMs) that mediate interactions with its UG-rich RNA targets reveals a new RRM arrangement critical for TDP-43 function. TDP-43 encodes an alternative-splicing regulator with tandem RNA-recognition motifs (RRMs). The protein regulates cystic fibrosis transmembrane regulator ( CFTR ) exon 9 splicing through binding to long UG-rich RNA sequences and is found in cytoplasmic inclusions of several neurodegenerative diseases. We solved the solution structure of the TDP-43 RRMs in complex with UG-rich RNA. Ten nucleotides are bound by both RRMs, and six are recognized sequence specifically. Among these, a central G interacts with both RRMs and stabilizes a new tandem RRM arrangement. Mutations that eliminate recognition of this key nucleotide or crucial inter-RRM interactions disrupt RNA binding and TDP-43–dependent splicing regulation. In contrast, point mutations that affect base-specific recognition in either RRM have weaker effects. Our findings reveal not only how TDP-43 recognizes UG repeats but also how RNA binding–dependent inter-RRM interactions are crucial for TDP-43 function.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/337/1645/1792 / 631/45/500 / 631/535/878/1263 / Amino Acid Sequence / Base Composition / Binding proteins / Binding Sites / Biochemistry / Biological Microscopy / Cystic fibrosis / Cystic Fibrosis Transmembrane Conductance Regulator - genetics / Cystic Fibrosis Transmembrane Conductance Regulator - metabolism / DNA-Binding Proteins - chemistry / DNA-Binding Proteins - metabolism / DNA-Binding Proteins - physiology / Genetic regulation / Humans / Identification and classification / Life Sciences / Membrane Biology / Models, Molecular / Molecular Sequence Data / Molecular structure / Mutation / Neurodegeneration / Nuclear Magnetic Resonance, Biomolecular / Protein Structure / Protein Structure, Tertiary / Proteins / Ribonucleic acid / RNA / RNA splicing / RNA Splicing - physiology / RNA-Binding Proteins - chemistry / RNA-Binding Proteins - metabolism / RNA-Binding Proteins - physiology