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

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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 (Lead / Corresponding author); Brown, John W. S. (Lead / Corresponding author).

In: Nucleic Acids Research, Vol. 40, No. 6, 03.2012, p. 2454-2469.

Research output: Contribution to journalArticle

Harvard

Kalyna, M, Simpson, CG, Syed, NH, Lewandowska, D, Marquez, Y, Kusenda, B, Marshall, J, Fuller, J, Cardle, L, McNicol, J, Dinh, HQ, Barta, A & Brown, JWS 2012, 'Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis' Nucleic Acids Research, vol 40, no. 6, pp. 2454-2469., 10.1093/nar/gkr932

APA

Kalyna, M., Simpson, C. G., Syed, N. H., Lewandowska, D., Marquez, Y., Kusenda, B., ... 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. 10.1093/nar/gkr932

Vancouver

Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B et al. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Research. 2012 Mar;40(6):2454-2469. Available from: 10.1093/nar/gkr932

Author

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 (Lead / Corresponding author); Brown, John W. S. (Lead / Corresponding author) / Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis.

In: Nucleic Acids Research, Vol. 40, No. 6, 03.2012, p. 2454-2469.

Research output: Contribution to journalArticle

Bibtex - Download

@article{4adfb69093ed4055a5d38584814d3310,
title = "Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis",
author = "Maria Kalyna and Simpson, {Craig G.} and Syed, {Naeem H.} and Dominika Lewandowska and Yamile Marquez and Branislav Kusenda and Jacqueline Marshall and John Fuller and Linda Cardle and Jim McNicol and Dinh, {Huy Q.} and Andrea Barta and Brown, {John W. S.}",
year = "2012",
doi = "10.1093/nar/gkr932",
volume = "40",
number = "6",
pages = "2454--2469",
journal = "Nucleic Acids Research",
issn = "0305-1048",

}

RIS (suitable for import to EndNote) - Download

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 &gt; 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 &gt; 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>

UR - http://www.scopus.com/inward/record.url?scp=84859293997&partnerID=8YFLogxK

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 -

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