A Role for Nonsense-Mediated mRNA Decay in Plants: Pathogen Responses Are Induced in Arabidopsis thaliana NMD Mutants

Rayson, Samantha; Arciga-Reyes, Luis; Wootton, Lucie; Zabala, Marta de Torres; Truman, William; Graham, Neil; Grant, Murray; Davies, Brendan

doi:10.1371/journal.pone.0031917

Cited by 115 publications

(151 citation statements)

References 108 publications

(157 reference statements)

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“…2d and Table 2), similar to the percentage of nonsense-mediated decay (NMD)-controlled genes in a wide range of species 33,34 . Premature termination codons activate the NMD pathway 35 , which leads to rapid degradation of PTC1 transcripts, and have been associated with transcriptional regulation during disease and stress response in human and Arabidopsis, respectively 34,[36][37][38][39] . The distribution of PTC1 transcripts was strikingly dissimilar, both spatially and temporally, with only 7.4% shared and between 31% and 40% exclusively observed in only a single sample (Fig.…”

Section: Regulation Of Gene Expressionmentioning

confidence: 99%

A physical, genetic and functional sequence assembly of the barley genome

2012

Nature

1,277

853

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Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement

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Section: Regulation Of Gene Expressionmentioning

confidence: 99%

A physical, genetic and functional sequence assembly of the barley genome

2012

Nature

1,277

853

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“…In Arabidopsis, mutants in the homologs of the NMD components UP FRAMESHIFT1 (UPF1), UPF2, UPF3, and SMG7 show a higher resistance to P. syringae infection (Jeong et al, 2012;Rayson et al, 2012;Riehs-Kearnan et al, 2012;Shi et al, 2012). Among genes misexpressed in the upf1-5 and upf3-1 mutants, genes connected to pathogen response are enriched.…”

Section: Factors Involved In As Of R Genes and Plant Defensementioning

confidence: 99%

“…One may envisage that PTC-containing transcripts encoding putative truncated R gene products are stabilized for defense by downregulation of the NMD pathway. Clearly, a more detailed analysis is required to disentangle causes and consequences of the phenotypes: whether the increased level of defense-associated transcripts is due to an inhibition of mRNA degradation or an indirect consequence of elevated salicylic acid (SA) level in the mutants (Jeong et al, 2012;Rayson et al, 2012;Riehs-Kearnan et al, 2012).…”

Section: Factors Involved In As Of R Genes and Plant Defensementioning

confidence: 99%

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

2013

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High-throughput sequencing for transcript profiling in plants has revealed that alternative splicing (AS) affects a much higher proportion of the transcriptome than was previously assumed. AS is involved in most plant processes and is particularly prevalent in plants exposed to environmental stress. The identification of mutations in predicted splicing factors and spliceosomal proteins that affect cell fate, the circadian clock, plant defense, and tolerance/sensitivity to abiotic stress all point to a fundamental role of splicing/AS in plant growth, development, and responses to external cues. Splicing factors affect the AS of multiple downstream target genes, thereby transferring signals to alter gene expression via splicing factor/AS networks. The last two to three years have seen an ever-increasing number of examples of functional AS. At a time when the identification of AS in individual genes and at a global level is exploding, this review aims to bring together such examples to illustrate the extent and importance of AS, which are not always obvious from individual publications. It also aims to ensure that plant scientists are aware that AS is likely to occur in the genes that they study and that dynamic changes in AS and its consequences need to be considered routinely.

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“…Alternative splicing and transcription start sites have the potential to alter a transcript's sensitivity to NMD (Rayson et al, 2012). Although the rules governing which transcripts are sent through the NMD pathway remain to be fully elucidated, recent studies suggest that three major factors in plants include 39 untranslated regions (UTRs) longer than 350 nucleotides, exons within 39 UTRs, and open reading frames greater than 35 amino acids within 59 UTRs (Kalyna et al, 2012).…”

Section: Nmd Sensitivity Is Affected By Isoform Switching During Devementioning

confidence: 99%

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

et al. 2015

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Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage-or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.After transcription, the majority of eukaryotic premRNA is subjected to a series of posttranscriptional modifications, including the removal of introns to form a mature mRNA (Stamm et al., 2005). Although some introns are removed constitutively, many can be processed in a variety of alternative ways, including exon skipping, intron retention, alternative acceptor, alternative donor, and alternative position (change in both acceptor and donor positions; Lorkovic et al., 2000). These alternative splicing events form a crucial regulatory level and have the ability to alter an mRNA's stability, localization, and protein products. Alternative splicing events are controlled by a variety of cis-elements, including the presence of consensus splice sequences at the intron-exon border and intronic and exonic splicing enhancer sequences (Pertea et al., 2007). Trans-acting factors also exert a strong effect on splicing and are mostly composed of Ser/Arg-rich proteins, which typically promote intron removal, and heterogenous nuclear ribonucleoproteins, which typically inhibit it (Erkelenz et al., 2013). A host of other indirect factors can affect splicing, including transcription rate, methylation status, and any cellular conditions that alter RNA secondary structure (Kornblihtt et al

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A Role for Nonsense-Mediated mRNA Decay in Plants: Pathogen Responses Are Induced in Arabidopsis thaliana NMD Mutants

Cited by 115 publications

References 108 publications

A physical, genetic and functional sequence assembly of the barley genome

A physical, genetic and functional sequence assembly of the barley genome

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

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