Characterization and functional implications of the RNA binding properties of nuclear factor TDP-43, a novel splicing regulator of CFTR exon 9

J Biol Chem. 2001 Sep 28;276(39):36337-43. doi: 10.1074/jbc.M104236200. Epub 2001 Jul 24.

Abstract

Variations in a polymorphic (TG)m sequence near exon 9 of the human CFTR gene have been associated with variable proportions of exon skipping and occurrence of disease. We have recently identified nuclear factor TDP-43 as a novel splicing regulator capable of binding to this element in the CFTR pre-mRNA and inhibiting recognition of the neighboring exon. In this study we report the dissection of the RNA binding properties of TDP-43 and their functional implications in relationship with the splicing process. Our results show that this protein contains two fully functional RNA recognition motif (RRM) domains with distinct RNA/DNA binding characteristics. Interestingly, TDP-43 can bind a minimum number of six UG (or TG) single-stranded dinucleotide stretches, and binding affinity increases with the number of repeats. In particular, the highly conserved Phe residues in the first RRM region play a key role in nucleic acid recognition.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing*
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Binding, Competitive
  • Cell Nucleus / metabolism*
  • Cystic Fibrosis Transmembrane Conductance Regulator / genetics
  • Cystic Fibrosis Transmembrane Conductance Regulator / metabolism*
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry*
  • Exons
  • Gene Deletion
  • Glutathione Transferase / metabolism
  • Humans
  • Molecular Sequence Data
  • Mutation
  • Nucleic Acids / metabolism
  • Oligonucleotides / metabolism
  • Phenylalanine / chemistry
  • Plasmids / metabolism
  • Polymorphism, Genetic
  • Protein Binding
  • Protein Structure, Tertiary
  • RNA / metabolism
  • RNA, Messenger / metabolism
  • Recombinant Fusion Proteins / metabolism
  • Recombinant Proteins / metabolism
  • Sequence Homology, Amino Acid
  • Ultraviolet Rays

Substances

  • CFTR protein, human
  • DNA-Binding Proteins
  • Nucleic Acids
  • Oligonucleotides
  • RNA, Messenger
  • Recombinant Fusion Proteins
  • Recombinant Proteins
  • Cystic Fibrosis Transmembrane Conductance Regulator
  • Phenylalanine
  • RNA
  • DNA
  • Glutathione Transferase

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