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Updated: Aug 13, 2026

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
Published on: September 28, 2017
Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p
Tzvi Aviv1, Zhen Lin, Giora Ben-Ari
1Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave., Toronto, Ontario, M5G 1X5, Canada.
Abstract:
The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1p epitomizes a subfamily of SAM domains conserved from yeast to humans that function as sequence-specific RNA-binding domains. Here we report the 2.0-A X-ray structure of the Vts1p SAM domain bound to a high-affinity RNA ligand. Specificity of RNA binding arises from the association of a guanosine loop base with a shallow pocket on the SAM domain and from multiple SAM domain contacts to the unique backbone structure of the loop, defined in part by a nonplanar base pair within the loop. We have validated NNF1 as an endogenous target of Vts1p among 79 transcripts that copurify with Vts1p. Bioinformatic analysis of these mRNAs demonstrates that the RNA-binding specificity of Vts1p in vivo is probably more stringent than that of the isolated SAM domain in vitro.
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