Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. / 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.
In: Nucleic Acids Research, Vol. 40, No. 6, 03.2012, p. 2454-2469.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis
A1 - Kalyna,Maria
A1 - Simpson,Craig G.
A1 - Syed,Naeem H.
A1 - Lewandowska,Dominika
A1 - Marquez,Yamile
A1 - Kusenda,Branislav
A1 - Marshall,Jacqueline
A1 - Fuller,John
A1 - Cardle,Linda
A1 - McNicol,Jim
A1 - Dinh,Huy Q.
A1 - Barta,Andrea
A1 - Brown,John W. S.
AU - Kalyna,Maria
AU - Simpson,Craig G.
AU - Syed,Naeem H.
AU - Lewandowska,Dominika
AU - Marquez,Yamile
AU - Kusenda,Branislav
AU - Marshall,Jacqueline
AU - Fuller,John
AU - Cardle,Linda
AU - McNicol,Jim
AU - Dinh,Huy Q.
AU - Barta,Andrea
AU - Brown,John W. S.
PY - 2012/3
Y1 - 2012/3
N2 - <p>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.</p>
AB - <p>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.</p>
U2 - 10.1093/nar/gkr932
DO - 10.1093/nar/gkr932
M1 - Article
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 6
VL - 40
SP - 2454
EP - 2469
ER -