Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43.
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.
1] Central European Institute of Technology, Masaryk University, Brno, Czech Republic. [2] Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Hönggerberg, Zürich, Switzerland.
Peter J
PJ
Lukavsky
Dalia
D
Daujotyte
James R
JR
Tollervey
Jernej
J
Ule
Cristiana
C
Stuani
Emanuele
E
Buratti
Francisco E
FE
Baralle
Fred F
FF
Damberger
Frédéric H-T
FH
Allain
D000595:Amino Acid Sequence; D001482:Base Composition; D001665:Binding Sites; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D017434:Protein Structure, Tertiary; D012326:RNA Splicing / Q000502:physiology*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*
C505032:CFTR protein, human; D004268:DNA-Binding Proteins; D016601:RNA-Binding Proteins; D019005:Cystic Fibrosis Transmembrane Conductance Regulator