title: 3' Rapid Amplification of cDNA Ends (3' RACE) UsingArabidopsisSamples.
abstract: Production of functional eukaryotic RNA is a very elaborate process that involves a complex interplay between transcription and various RNA processing activities, including splicing, 5' capping, and 3' cleavage and polyadenylation (Bentley, 2014). Accurate mapping of RNA ends provides a valuable tool to assess transcriptional and post-transcriptional events giving rise to different gene transcripts. The abundance of such transcripts most likely depends on exogenous and developmental cues, or mutations. In the reference plantArabidopsis, perturbation of theHUA-PEPpost-transcriptional regulatory factors (Rodríguez-Cazorlaet al., 2015) leads to the accumulation of aberrant transcripts of the key floral homeotic geneAGAMOUS(AG) (Yanofskyet al., 1990) that retain intronic sequence. It was determined by 3' RACE reactions that such erroneous transcripts correspond to premature processing and polyadenylation events taking place at theAGintron region. Here we describe a protocol that is suitable for analysis of relatively abundant transcripts and also for detecting aberrant RNA species that are likely prone to rapid turnover. Likewise, the method, here adapted toArabidopsisreproductive tissues, can be applied to characterize RNA species from other organs (leaf, root) and/or other plant species. We provide a detailed protocol of our 3' RACE procedure comprising four major parts: Total RNA extraction, RNA amount determination and quality control, the RACE procedure itself, and isolation of the resulting RACE products for cloning and sequencing.
authors.affiliation: Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d'Alacant, Sant Joan d'Alacant, Alicante, Spain.
authors.forename: Encarnación
authors.initials: E
authors.lastname: Rodríguez-Cazorla
authors.affiliation: Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d'Alacant, Sant Joan d'Alacant, Alicante, Spain.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Andújar
authors.affiliation: Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, USA.
authors.forename: Juan José
authors.initials: JJ
authors.lastname: Ripoll
authors.affiliation: Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, USA.
authors.forename: Lindsay J
authors.initials: LJ
authors.lastname: Bailey
authors.affiliation: Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d'Alacant, Sant Joan d'Alacant, Alicante, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Martínez-Laborda
authors.affiliation: Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, USA.
authors.forename: Martin F
authors.initials: MF
authors.lastname: Yanofsky
authors.affiliation: Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d'Alacant, Sant Joan d'Alacant, Alicante, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Vera