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Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis
- Source :
- Nucleic Acids Research
- Publication Year :
- 2011
- Publisher :
- Oxford University Press (OUP), 2011.
-
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.
- Subjects :
- 0106 biological sciences
Untranslated region
Nonsense-mediated decay
Arabidopsis
Codon, Initiator
Gene Regulation, Chromatin and Epigenetics
Biology
Genes, Plant
01 natural sciences
03 medical and health sciences
Gene Expression Regulation, Plant
Genes, Regulator
Genetics
Protein Isoforms
RNA, Messenger
Cycloheximide
3' Untranslated Regions
Gene
030304 developmental biology
Regulator gene
0303 health sciences
Arabidopsis Proteins
Reverse Transcriptase Polymerase Chain Reaction
Alternative splicing
Intron
biology.organism_classification
Introns
Nonsense Mediated mRNA Decay
Alternative Splicing
Open reading frame
Codon, Nonsense
RNA Helicases
010606 plant biology & botany
Subjects
Details
- ISSN :
- 13624962 and 03051048
- Volume :
- 40
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi.dedup.....10763e1a816afed4a0b108191e5d9cfb