Regulation of gene expression by the action of a fungal lncRNA on a transactivator

Till, Petra; Derntl, Christian; Kiesenhofer, Daniel P.; Mach, Robert L.; Yaver, Debbie; Mach-Aigner, Astrid R.

doi:10.1080/15476286.2019.1663618

Cited by 12 publications

(8 citation statements)

References 39 publications

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“…Therefore, the prediction of lncRNA function depends on target gene prediction. Functional characterization of lncRNAs has revealed that both cis- and trans-acting lncRNAs have roles in gene regulation [ 21 , 25 ]. However, previous fungal lncRNA profiling studies considered only cis-acting lncRNAs [ 29 , 30 ].…”

Section: Discussionmentioning

confidence: 99%

“…Yeast lncRNAs modulate vegetative growth, sexual reproduction, cell–cell adhesion, and phosphate regulation [ 17 , 18 ]. LncRNAs also regulate the circadian clock ( qrf ) and cellulase genes ( HAX1 ) in the saprotrophic fungi Neurospora crassa and Trichoderma reesei , respectively [ 19 – 21 ]. LncRNA RZE1 regulates zinc finger transcription factor ZNF2 and affects the yeast-to-hypha transition in the human pathogenic fungus Cryptococcus neoformans [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

et al. 2022

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Background Long non-coding RNAs (lncRNAs) play essential roles in developmental processes and disease development at the transcriptional and post-transcriptional levels across diverse taxa. However, only few studies have profiled fungal lncRNAs in a genome-wide manner during host infection. Results Infection-associated lncRNAs were identified using lncRNA profiling over six stages of host infection (e.g., vegetative growth, pre-penetration, biotrophic, and necrotrophic stages) in the model pathogenic fungus, Magnaporthe oryzae. We identified 2,601 novel lncRNAs, including 1,286 antisense lncRNAs and 980 intergenic lncRNAs. Among the identified lncRNAs, 755 were expressed in a stage-specific manner and 560 were infection-specifically expressed lncRNAs (ISELs). To decipher the potential roles of lncRNAs during infection, we identified 365 protein-coding genes that were associated with 214 ISELs. Analysis of the predicted functions of these associated genes suggested that lncRNAs regulate pathogenesis-related genes, including xylanases and effectors. Conclusions The ISELs and their associated genes provide a comprehensive view of lncRNAs during fungal pathogen-plant interactions. This study expands new insights into the role of lncRNAs in the rice blast fungus, as well as other plant pathogenic fungi.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

et al. 2022

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“…Thus, carP may act on other regulatory protein through a mechanism like that described for the HAX1 lncRNA of T. reesei [24]. HAX1 is a transactivator of cellulase expression that forms an RNA-protein complex with the regulatory protein Xyr1 [25].…”

Section: Discussionmentioning

confidence: 99%

The carP lncRNA Is a carS-Related Regulatory Element with Broad Effects on the Fusarium fujikuroi Transcriptome

Pardo-Medina¹,

Gutiérrez²,

Limón³

et al. 2021

ncRNA

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Carotenoid biosynthesis in the fungus Fusarium fujikuroi is regulated by environmental factors, with light being the main stimulating signal. The CarS RING-finger protein plays an important role in the downregulation of structural genes of the carotenoid pathway. A recent transcriptomic analysis on the effect of carS mutation identified a gene for a long non-coding RNA (lncRNA) upstream of carS, called carP, the deletion of which results in increased carS mRNA levels and lack of carotenoid production. We have investigated the function of carP by studying the transcriptomic effect of its deletion and the phenotypes resulting from the reintroduction of carP to a deletion strain. The RNA-seq data showed that the loss of carP affected the mRNA levels of hundreds of genes, especially after illumination. Many of these changes appeared to be cascade effects as a result of changes in carS expression, as suggested by the comparison with differentially expressed genes in a carS mutant. Carotenoid production only recovered when carP was integrated upstream of carS, but not at other genomic locations, indicating a cis-acting mechanism on carS. However, some genes hardly affected by CarS were strongly upregulated in the carP mutant, indicating that carP may have other regulatory functions as an independent regulatory element.

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“…Therefore, the prediction of lncRNA function depends on target gene prediction. Functional characterization o ncRNAs has revealed that both cis-and trans-actinglncRNAs have roles in gene regulation [21,25]. However, previous fungal lncRNA pro ling studies considered only cis-acting lncRNAs [29,30].…”

Section: Discussionmentioning

confidence: 99%

“…Yeast lncRNAs modulate vegetative growth, sexual reproduction, cell-cell adhesion, and phosphate regulation [17,18]. LncRNAs also regulate the circadian clock (qrf) and cellulase genes (HAX1) in the saprotrophic fungi Neurospora crassa and Trichoderma reesei, respectively [19][20][21]. LncRNA RZE1 regulates zinc nger transcription factor ZNF2 and affects the yeast-to-hypha transition in the human pathogenic fungus Cryptococcus neoformans [22].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Profiling of Long Non-coding RNA of the Rice Blast Fungus Magnaporthe oryzae During Infection

Choi

Jeon

Lee

et al. 2021

Preprint

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BackgroundLong non-coding RNAs (lncRNAs) play essential roles in developmental processes and disease development at the transcriptional and post-transcriptional levels across diverse taxa. However, only few studies have profiled fungal lncRNAs in a genome-wide manner during host infection.ResultsInfection-associated lncRNAs were identified using lncRNA profiling over six stages of host infection (e.g., vegetative growth, pre-penetration, biotrophic, and necrotrophic stages) in the model pathogenic fungus, Magnaporthe oryzae. We identified 2,601 novel lncRNAs, including 1,286 antisense lncRNAs and 980 intergenic lncRNAs. Among the identified lncRNAs, 755 were expressed in a stage-specific manner and 560 were infection-specifically expressed lncRNAs (ISELs). To decipher the potential roles of lncRNAs during infection, we identified 365 protein-coding genes that were associated with 214 ISELs. Analysis of the predicted functions of these associated genes suggested that lncRNAs regulate pathogenesis-related genes, including xylanases and effectors.ConclusionsThe ISELs and their associated genes provide a comprehensive view of lncRNAs during fungal pathogen-plant interactions. This study expands new insights into the role of lncRNAs in the rice blast fungus, as well as other plant pathogenic fungi.

show abstract

Regulation of gene expression by the action of a fungal lncRNA on a transactivator

Cited by 12 publications

References 39 publications

Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

The carP lncRNA Is a carS-Related Regulatory Element with Broad Effects on the Fusarium fujikuroi Transcriptome

Genome-wide Profiling of Long Non-coding RNA of the Rice Blast Fungus Magnaporthe oryzae During Infection

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