Details

Autor(en) / Beteiligte

• Kalyna, Maria
• Simpson, Craig G
• Syed, Naeem H
• Lewandowska, Dominika
• Marquez, Yamile
• Kusenda, Branislav
• Marshall, Jacqueline
• Fuller, John
• Cardle, Linda
• McNicol, Jim
• Dinh, Huy Q
• Barta, Andrea
• Brown, John W S

Titel

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

Ist Teil von

• Nucleic acids research, 2012-03, Vol.40 (6), p.2454-2469

Ort / Verlag

England

Erscheinungsjahr

2012

Quelle

MEDLINE

Beschreibungen/Notizen

• 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.