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Article
An antisense microwalk reveals critical role of an intronic position linked to a unique long-distance interaction in pre-mRNA splicing
RNA
  • Natalia N. Singh, Iowa State University
  • Katrin Hollinger, Iowa State University
  • Dhruva Bhattacharya, Iowa State University
  • Ravindra N. Singh, Iowa State University
Document Type
Article
Publication Version
Published Version
Publication Date
1-1-2010
DOI
10.1261/rna.2154310
Abstract
Here we report a novel finding of an antisense oligonucleotide (ASO) microwalk in which we examined the position-specific role of intronic residues downstream from the 5′ splice site (5′ ss) of SMN2 exon 7, skipping of which is associated with spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. Our results revealed the inhibitory role of a cytosine residue at the 10th intronic position (10C), which is neither conserved nor associated with any known splicing motif. Significance of 10C emerged from the splicing pattern of SMN2 exon 7 in presence of a 14-mer ASO (L14) that sequestered two adjacent hnRNP A1 motifs downstream from 10C and yet promoted SMN2 exon 7 skipping. Another 14-mer ASO (F14) that sequestered both, 10C and adjacent hnRNP A1 motifs, led to a strong stimulation of SMN2 exon 7 inclusion. The inhibitory role of 10C was found to be tightly linked to its unpaired status and specific positioning immediately upstream of a RNA:RNA helix formed between the targeting ASO and its intronic target. Employing a heterologous context as well as changed contexts of SMN2 intron 7, we show that the inhibitory effect of unpaired 10C is dependent upon a long-distance interaction involving downstream intronic sequences. Our report furnishes one of the rare examples in which an ASO-based approach could be applied to unravel the critical role of an intronic position that may not belong to a linear motif and yet play significant role through long-distance interactions.
Comments

This is an article from RNA 16 (2010): 1167, doi:10.1261/rna.2154310. Posted with permission.

Copyright Owner
RNA Society
Language
en
File Format
application/pdf
Citation Information
Natalia N. Singh, Katrin Hollinger, Dhruva Bhattacharya and Ravindra N. Singh. "An antisense microwalk reveals critical role of an intronic position linked to a unique long-distance interaction in pre-mRNA splicing" RNA Vol. 16 (2010) p. 1167 - 1181
Available at: http://works.bepress.com/ravindra-singh/2/