Journal
NUCLEIC ACIDS RESEARCH
Volume 40, Issue 6, Pages 2454-2469Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkr932
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Funding
- Biotechnology and Biological Sciences Research Council (BBSRC) [BB/G000212/1]
- Biotechnology and Biological Sciences Research Council (BBSRC) [ERA-NET Plant Genomics (PASAS)] [BB/G024979/1]
- Scottish Government Rural and Environment Research and Analysis Directorate (RERAD) [WP114]
- EU FP6 Programme Network of Excellence on Alternative Splicing (EURASNET) [LSHG-CT-2005-518238]
- Austrian Science Fund (FWF) [SFB 1710, 1711, DK W1207]
- Austrian Science Fund (FWF) [ERA-NET Plant Genomics (PASAS)] [I254]
- Austria Genomic Program (GENAU II, III
- ncRNAs)
- WWTF Science Chair
- Austrian National Science Foundation (FWF)
- BBSRC [BB/G000212/1, BB/G024979/1] Funding Source: UKRI
- Austrian Science Fund (FWF) [I 254] Funding Source: researchfish
- Biotechnology and Biological Sciences Research Council [BB/G000212/1, BB/G024979/1] Funding Source: researchfish
- Austrian Science Fund (FWF) [I254, W1207] Funding Source: Austrian Science Fund (FWF)
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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.
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