title: Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis.
abstract: Alternative splicing (AS) coupled to nonsense-mediated decay (NMD) is a post-transcriptional mechanism for regulating gene expression. We have used a high-resolution AS RT-PCR panel to identify endogenous AS isoforms which increase in abundance when NMD is impaired in the Arabidopsis NMD factor mutants, upf1-5 and upf3-1. Of 270 AS genes (950 transcripts) on the panel, 102 transcripts from 97 genes (32%) were identified as NMD targets. Extrapolating from these data around 13% of intron-containing genes in the Arabidopsis genome are potentially regulated by AS/NMD. This cohort of naturally occurring NMD-sensitive AS transcripts also allowed the analysis of the signals for NMD in plants. We show the importance of AS in introns in 5' or 3'UTRs in modulating NMD-sensitivity of mRNA transcripts. In particular, we identified upstream open reading frames overlapping the main start codon as a new trigger for NMD in plants and determined that NMD is induced if 3'-UTRs were >350 nt. Unexpectedly, although many intron retention transcripts possess NMD features, they are not sensitive to NMD. Finally, we have shown that AS/NMD regulates the abundance of transcripts of many genes important for plant development and adaptation including transcription factors, RNA processing factors and stress response genes.
authors: Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria.
authors: Maria
authors: M
authors: Kalyna
authors: Craig G
authors: CG
authors: Simpson
authors: Naeem H
authors: NH
authors: Syed
authors: Dominika
authors: D
authors: Lewandowska
authors: Yamile
authors: Y
authors: Marquez
authors: Branislav
authors: B
authors: Kusenda
authors: Jacqueline
authors: J
authors: Marshall
authors: John
authors: J
authors: Fuller
authors: Linda
authors: L
authors: Cardle
authors: Jim
authors: J
authors: McNicol
authors: Huy Q
authors: HQ
authors: Dinh
authors: Andrea
authors: A
authors: Barta
authors: John W S
authors: JW
authors: Brown
mesh_terms: D020413:3' Untranslated Regions; D017398:Alternative Splicing; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D018387:Codon, Initiator; D018389:Codon, Nonsense; D003513:Cycloheximide / Q000494:pharmacology; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005809:Genes, Regulator; D007438:Introns; D059365:Nonsense Mediated mRNA Decay / Q000187:drug effects; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D020365:RNA Helicases / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D020413:3' Untranslated Regions; D029681:Arabidopsis Proteins; D018387:Codon, Initiator; D018389:Codon, Nonsense; D020033:Protein Isoforms; D012333:RNA, Messenger; C504799:UPF3 protein, Arabidopsis; D003513:Cycloheximide; C513125:UPF1 protein, Arabidopsis; D020365:RNA Helicases