title: Complexity of the alternative splicing landscape in plants.
abstract: Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
authors.affiliation: Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523.
authors.forename: Anireddy S N
authors.initials: AS
authors.lastname: Reddy
authors.forename: Yamile
authors.initials: Y
authors.lastname: Marquez
authors.forename: Maria
authors.initials: M
authors.lastname: Kalyna
authors.forename: Andrea
authors.initials: A
authors.lastname: Barta
mesh_terms: D017398:Alternative Splicing; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D063245:Plant Development; D012322:RNA Precursors / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D015398:Signal Transduction; D017381:Spliceosomes / Q000378:metabolism
chemical_list: D012322:RNA Precursors; D018749:RNA, Plant