Synthetic oligonucleotides recruit ILF2/3 to RNA transcripts to modulate splicing

Nat Chem Biol. 2012 Apr 15;8(6):555-61. doi: 10.1038/nchembio.939.

Abstract

We describe a new technology for recruiting specific proteins to RNA through selective recognition of heteroduplexes formed with chemically modified antisense oligonucleotides (ASOs). Typically, ASOs function by hybridizing to their RNA targets and blocking the binding of single-stranded RNA-binding proteins. Unexpectedly, we found that ASOs with 2'-deoxy-2'-fluoro (2'-F) nucleotides, but not with other 2' chemical modifications, have an additional property: they form heteroduplexes with RNA that are specifically recognized by the interleukin enhancer-binding factor 2 and 3 complex (ILF2/3). 2'-F ASO-directed recruitment of ILF2/3 to RNA can be harnessed to control gene expression by modulating alternative splicing of target transcripts. ILF2/3 recruitment to precursor mRNA near an exon results in omission of the exon from the mature mRNA, both in cell culture and in mice. We discuss the possibility of using chemically engineered ASOs that recruit specific proteins to modulate gene expression for therapeutic intervention.

MeSH terms

  • Alternative Splicing / drug effects*
  • Alternative Splicing / genetics
  • Animals
  • Binding Sites
  • Exons
  • Fibroblasts / drug effects
  • Fibroblasts / metabolism
  • HeLa Cells
  • Humans
  • Mice
  • Mice, Knockout
  • Muscular Atrophy, Spinal / genetics
  • Muscular Atrophy, Spinal / metabolism
  • Nuclear Factor 45 Protein / genetics
  • Nuclear Factor 45 Protein / metabolism*
  • Nuclear Factor 90 Proteins / genetics
  • Nuclear Factor 90 Proteins / metabolism*
  • Oligonucleotides, Antisense / chemistry
  • Oligonucleotides, Antisense / genetics
  • Oligonucleotides, Antisense / pharmacology*
  • RNA Precursors / genetics
  • RNA Precursors / metabolism*
  • RNA Splice Sites
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Survival of Motor Neuron 1 Protein / genetics
  • Survival of Motor Neuron 2 Protein / genetics
  • Transfection

Substances

  • ILF2 protein, human
  • ILF3 protein, human
  • Nuclear Factor 45 Protein
  • Nuclear Factor 90 Proteins
  • Oligonucleotides, Antisense
  • RNA Precursors
  • RNA Splice Sites
  • RNA, Messenger
  • SMN1 protein, human
  • SMN2 protein, human
  • Survival of Motor Neuron 1 Protein
  • Survival of Motor Neuron 2 Protein