Alternative Splicing and DNA Damage Response in Plants

Nimeth, Barbara A; Riegler, Stefan; Kalyna, Maria

doi:10.3389/fpls.2020.00091

Cited by 24 publications

(12 citation statements)

References 108 publications

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“…Thus, upon replicative stress, the intron retention on these CYCDs results in altered proteins unable to activate CDKA;1 leading to an arrest of cell cycle progression [124]. Similarly to the animal field [130], and given that among others, SOG1, ATM and ATR, are also subject to alternative splicing, these data further support the implication of alternative splicing in the plant DDR control (reviewed in [131]).…”

Section: Wee1 a Key Intra-s Checkpoint Proteinmentioning

confidence: 67%

Connections between the Cell Cycle and the DNA Damage Response in Plants

Gentric

Genschik

Noir

2021

IJMS

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Due to their sessile lifestyle, plants are especially exposed to various stresses, including genotoxic stress, which results in altered genome integrity. Upon the detection of DNA damage, distinct cellular responses lead to cell cycle arrest and the induction of DNA repair mechanisms. Interestingly, it has been shown that some cell cycle regulators are not only required for meristem activity and plant development but are also key to cope with the occurrence of DNA lesions. In this review, we first summarize some important regulatory steps of the plant cell cycle and present a brief overview of the DNA damage response (DDR) mechanisms. Then, the role played by some cell cycle regulators at the interface between the cell cycle and DNA damage responses is discussed more specifically.

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Section: Wee1 a Key Intra-s Checkpoint Proteinmentioning

confidence: 67%

Connections between the Cell Cycle and the DNA Damage Response in Plants

Gentric

Genschik

Noir

2021

IJMS

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“…Therefore, we expected the enrichment of the mRNA surveillance pathway and spliceosome pathway in the DSGs ( Figure 5 ). In addition, base excision repair related genes are known to play a crucial role in repair of a variety of DNA lesions ( Nimeth et al 2020 ). Notably, several genes encoding base excision repair proteins were significantly enriched in the DSGs ( Figure 5 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of the soybean root transcriptome reveals the impact of nitrate on alternative splicing

Guo

Dai

Chen

et al. 2021

G3 Genes|Genomes|Genetics

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In plants, nitrate acts not only as a signaling molecule that affects plant development but also as a nutrient. The development of plant roots, which directly absorb nutrients, is greatly affected by nitrate supply. Alternative gene splicing plays a crucial role in the plant stress response by increasing transcriptome diversity. The effects of nitrate supply on alternative splicing (AS), however, have not been investigated in soybean roots. We used high-quality high-throughput RNA-sequencing data to investigate genome-wide AS events in soybean roots in response to various levels of nitrate supply. In total, we identified 355 nitrate-responsive AS events between optimal and high nitrate levels (NH), 335 nitrate-responsive AS events between optimal and low nitrate levels (NL), and 588 nitrate-responsive AS events between low and high nitrate levels (NLH). RI and A3SS were the most common AS types; in particular, they accounted for 67% of all AS events under all conditions. This increased complex and diversity of AS events regulation might be associated with the soybean response to nitrate. Functional ontology enrichment analysis suggested that the differentially splicing genes were associated with several pathways, including spliceosome, base excision repair, mRNA surveillance pathway and so on. Finally, we validated several AS events using reverse transcription–polymerase chain reaction to confirm our RNA-seq results. In summary, we characterized the features and patterns of genome-wide AS in the soybean root exposed to different nitrate levels, and our results revealed that AS is an important mechanism of nitrate-response regulation in the soybean root.

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“…However, 6.12% of the total genes were upregulated in the transcriptome data whereas downregulated in the proteomics data. This might result from transcriptional and post-transcriptional regulation, such as alternative splicing and miRNA regulation [44][45][46]. On the other hand, about 2.63% of the total genes were downregulated in transcriptome but upregulated in proteomics analysis, which was putatively due to the translation control mechanism [47].…”

Section: Amino Acid Transporters May Be Involved In Efficient N Remobmentioning

confidence: 99%

Integrated Transcriptional and Proteomic Profiling Reveals Potential Amino Acid Transporters Targeted by Nitrogen Limitation Adaptation

Liao

Tang

Zhou

et al. 2020

IJMS

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Nitrogen (N) is essential for plant growth and crop productivity. Organic N is a major form of remobilized N in plants’ response to N limitation. It is necessary to understand the regulatory role of N limitation adaption (NLA) in organic N remobilization for this adaptive response. Transcriptional and proteomic analyses were integrated to investigate differential responses of wild-type (WT) and nla mutant plants to N limitation and to identify the core organic N transporters targeted by NLA. Under N limitation, the nla mutant presented an early senescence with faster chlorophyll loss and less anthocyanin accumulation than the WT, and more N was transported out of the aging leaves in the form of amino acids. High-throughput transcriptomic and proteomic analyses revealed that N limitation repressed genes involved in photosynthesis and protein synthesis, and promoted proteolysis; these changes were higher in the nla mutant than in the WT. Both transcriptional and proteomic profiling demonstrated that LHT1, responsible for amino acid remobilization, were only significantly upregulated in the nla mutant under N limitation. These findings indicate that NLA might target LHT1 and regulate organic N remobilization, thereby improving our understanding of the regulatory role of NLA on N remobilization under N limitation.

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Alternative Splicing and DNA Damage Response in Plants

Cited by 24 publications

References 108 publications

Connections between the Cell Cycle and the DNA Damage Response in Plants

Connections between the Cell Cycle and the DNA Damage Response in Plants

Genome-wide analysis of the soybean root transcriptome reveals the impact of nitrate on alternative splicing

Integrated Transcriptional and Proteomic Profiling Reveals Potential Amino Acid Transporters Targeted by Nitrogen Limitation Adaptation

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