Arabidopsis RNA immunoprecipitation

• Published in: The Plant journal : for cell and molecular biology Vol. 59; no. 1; pp. 163 - 168
• Main Authors: Terzi, Lionel C, Simpson, Gordon G
• Format: Journal Article
• Language: English
• Published: Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01.07.2009; Blackwell Publishing Ltd; Blackwell
• Subjects: Arabidopsis; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Biological and medical sciences; Cellular biology; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation, Plant; Genomics; Immunoprecipitation - methods; Molecular and cellular biology; Molecular genetics; Plant biology; post-transcriptional; RNA; RNA immunoprecipitation; RNA, Plant - metabolism; RNA, Small Nuclear - genetics; RNA, Small Nuclear - metabolism; RNA-binding protein; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; RNA-protein interactions; Transcription. Transcription factor. Splicing. Rna processing; Arabidopsis thaliana; RNA-binding protein; RNA; Transcription; Cruciferae; Arabidopsis; Dicotyledones; Angiospermae; RNA binding protein; Spermatophyta; post-transcriptional; RNA immunoprecipitation
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313x.2009.03859.x

RNA-binding proteins are key regulators of plant gene expression. Consistent with this, the Arabidopsis genome encodes many RNA-binding proteins that are genetically required for normal development and for responding to environmental changes. However, the direct RNA targets and RNA processing events that these RNA-binding proteins control are poorly understood. In order to facilitate the functional characterization of RNA-binding proteins, we have applied the RNA immunoprecipitation assay to Arabidopsis. Working with the U2B"-U2 snRNA interaction as a model experimental system, we show that treatment of intact plants with formaldehyde allows immunocapture of U2 snRNA using antibodies that recognize U2B" fused to the generic GFP tag. When coupled with recent developments in whole-genome tiling arrays and high-throughput next-generation sequencing, this combination of procedures and technology has the potential to allow systematic functional analysis of plant RNA-binding proteins.