title: High-throughput nuclease-mediated probing of RNA secondary structure in plant transcriptomes.
abstract: Empirical measurement of RNA secondary structure is an invaluable tool that has provided a more complete understanding of the RNA life cycle and functionality of this extremely important molecule. In general, methods for probing structural information involve treating RNA with either a chemical or an enzyme that preferentially targets regions of the RNA in a single- or double-stranded conformation (ssRNA and dsRNA, respectively). Here, we describe an approach that utilizes a combination of ssRNA- and dsRNA-specific nuclease (ss- and dsRNase, respectively) treatments along with high-throughput sequencing technology to provide comprehensive and robust measurements of RNA secondary structure across entire plant transcriptomes.
authors.affiliation: Department of Biology, University of Pennsylvania, 433 S. University Ave., Philadelphia, PA, 19104, USA.
authors.forename: Lee E
authors.initials: LE
authors.lastname: Vandivier
authors.forename: Fan
authors.initials: F
authors.lastname: Li
authors.forename: Brian D
authors.initials: BD
authors.lastname: Gregory
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D009690:Nucleic Acid Conformation; D010944:Plants / Q000235:genetics*; D018749:RNA, Plant / Q000737:chemistry* / Q000235:genetics* / Q000302:isolation & purification; D012260:Ribonucleases / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D018749:RNA, Plant; D012260:Ribonucleases