title: Genomic SELEX: a discovery tool for genomic aptamers.
abstract: Genomic SELEX is a discovery tool for genomic aptamers, which are genomically encoded functional domains in nucleic acid molecules that recognize and bind specific ligands. When combined with genomic libraries and using RNA-binding proteins as baits, Genomic SELEX used with high-throughput sequencing enables the discovery of genomic RNA aptamers and the identification of RNA-protein interaction networks. Here we describe how to construct and analyze genomic libraries, how to choose baits for selections, how to perform the selection procedure and finally how to analyze the enriched sequences derived from deep sequencing. As a control procedure, we recommend performing a "Neutral" SELEX experiment in parallel to the selection, omitting the selection step. This control experiment provides a background signal for comparison with the positively selected pool. We also recommend deep sequencing the initial library in order to facilitate the final in silico analysis of enrichment with respect to the initial levels. Counter selection procedures, using modified or inactive baits, allow strengthening the binding specificity of the winning selected sequences.
authors.affiliation: Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Austria.
authors.forename: Bob
authors.initials: B
authors.lastname: Zimmermann
authors.forename: Ivana
authors.initials: I
authors.lastname: Bilusic
authors.forename: Christina
authors.initials: C
authors.lastname: Lorenz
authors.forename: Renée
authors.initials: R
authors.lastname: Schroeder
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D002874:Chromosome Mapping; D015698:Genomic Library; D012313:RNA / Q000737:chemistry*; D052156:SELEX Aptamer Technique
chemical_list: D052157:Aptamers, Nucleotide; D012313:RNA