Splice site strength-dependent activity and genetic buffering by poly-G runs

Nat Struct Mol Biol. 2009 Oct;16(10):1094-100. doi: 10.1038/nsmb.1661. Epub 2009 Sep 13.


Pre-mRNA splicing is regulated through the combinatorial activity of RNA motifs, including splice sites and splicing regulatory elements. Here we show that the activity of the G-run (polyguanine sequence) class of splicing enhancer elements is approximately 4-fold higher when adjacent to intermediate strength 5' splice sites (ss) than when adjacent to weak 5' ss, and approximately 1.3-fold higher relative to strong 5' ss. We observed this dependence on 5' ss strength in both splicing reporters and in global microarray and mRNA-Seq analyses of splicing changes following RNA interference against heterogeneous nuclear ribonucleoprotein (hnRNP) H, which cross-linked to G-runs adjacent to many regulated exons. An exon's responsiveness to changes in hnRNP H levels therefore depends in a complex way on G-run abundance and 5' ss strength. This pattern of activity enables G-runs and hnRNP H to buffer the effects of 5' ss mutations, augmenting both the frequency of 5' ss polymorphism and the evolution of new splicing patterns. Certain other splicing factors may function similarly.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alternative Splicing*
  • Amino Acid Motifs
  • Animals
  • Cross-Linking Reagents / metabolism
  • Exons
  • Genetic Techniques
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H / metabolism
  • Humans
  • Mice
  • Models, Genetic
  • Oligonucleotide Array Sequence Analysis
  • Poly G / genetics*
  • RNA Precursors / genetics
  • RNA Splicing
  • RNA, Messenger / metabolism


  • Cross-Linking Reagents
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H
  • RNA Precursors
  • RNA, Messenger
  • Poly G

Associated data

  • GEO/GSE12386
  • GEO/GSE16642