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

Maria Kalyna, Craig G. Simpson, Naeem H. Syed, Dominika Lewandowska, Yamile Marquez, Branislav Kusenda, Jacqueline Marshall, John Fuller, Linda Cardle, Jim McNicol, Huy Q. Dinh, Andrea Barta (Lead / Corresponding author), John W. S. Brown (Lead / Corresponding author)

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    231 Citations (Scopus)

    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.

    Original languageEnglish
    Pages (from-to)2454-2469
    Number of pages16
    JournalNucleic Acids Research
    Volume40
    Issue number6
    DOIs
    Publication statusPublished - Mar 2012

    Cite this

    Kalyna, M., Simpson, C. G., Syed, N. H., Lewandowska, D., Marquez, Y., Kusenda, B., Marshall, J., Fuller, J., Cardle, L., McNicol, J., Dinh, H. Q., Barta, A., & Brown, J. W. S. (2012). Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Research, 40(6), 2454-2469. https://doi.org/10.1093/nar/gkr932