An Overview on Identification and Regulatory Mechanisms of Long Non-coding RNAs in Fungi

Li, Juan; Liu, Xiaoying; Yin, Ziyu; Hú, Zhìhóng; Zhang, Ke‐Qin

doi:10.3389/fmicb.2021.638617

Cited by 15 publications

(13 citation statements)

References 144 publications

(195 reference statements)

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“…An overall review of the RNA section reveals that the lncRNAs are detected and assessed through high throughput sequencing, and bioinformatics approaches [ 20 ]. Similarly, several publications have identified lncRNAs implicated in bolting.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa

et al. 2023

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Background Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although bolting/flowering responsive genes have been identified in most sensitive and non-sensitive species, non-coding RNA molecules like long non-coding RNAs (lncRNAs) have not been investigated in lettuce. Hence, in this study, potential long non-coding RNAs that regulate flowering /bolting were investigated in two lettuce strains S24 (resistant strain) and S39 (susceptible strain) in different flowering times to better understand the regulation of lettuce bolting mechanism. For this purpose, we used two RNA-seq datasets to discover the lncRNA transcriptome profile during the transition from vegetative to reproductive phase. Results For identifying unannotated transcripts in these datasets, a 7-step pipeline was employed to filter out these transcripts and terminate with 293 novel lncRNAs predicted by PLncPRO and CREMA. These transcripts were then utilized to predict cis and trans flowering-associated targets and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Computational predictions of target gene function showed the involvement of putative flowering-related genes and enrichment of the floral regulators FLC, CO, FT, and SOC1 in both datasets. Finally, 17 and 18 lncRNAs were proposed as competing endogenous target mimics (eTMs) for novel and known lncRNA miRNAs, respectively. Conclusion Overall, this study provides new insights into lncRNAs that control the flowering time of plants known for bolting, such as lettuce, and opens new windows for further study.

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Section: Introductionmentioning

confidence: 99%

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa

et al. 2023

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“…LncRNAs modulate gene expression at the transcriptional and post-transcriptional levels; they have important roles in various metabolic pathways throughout eukaryotic species [ 39 ]. Most lncRNA studies have been performed in model yeasts, while the functional characterization and profiling of plant pathogen lncRNAs have been rarely studied [ 17 , 18 ]. Genome-wide profiling of plant pathogen lncRNAs in the disease process has been performed in the rice smut fungus U .…”

Section: Discussionmentioning

confidence: 99%

“…Functional analysis of lncRNAs in fungi has mainly been carried out in the yeast species, Saccharomyces cerevisiae and Schizosaccharomyces pombe . 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 ].…”

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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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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“…Although studies of lncRNAs in fungi are not as abundant as in other kingdoms of life, there is evidence that lncRNAs have regulatory roles in many fungal species ( Chacko and Lin, 2013 ; Till et al., 2018 ; Dhingra, 2020 ; Li et al., 2021 ). A majority of the knowledge on lncRNAs in fungi comes from the model yeasts S. cerevisiae and S. pombe ( Yamashita et al., 2016 ).…”

Section: Non-coding Rnas In Fungal Pathogensmentioning

confidence: 99%

Long Non-Coding RNAs in Cryptococcus neoformans: Insights Into Fungal Pathogenesis

Kalem

Panepinto

2022

Front. Cell. Infect. Microbiol.

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Long non-coding RNAs (lncRNAs) are highly expressed and can modulate multiple cellular processes including transcription, splicing, translation, and many diverse signaling events. LncRNAs can act as sponges for miRNAs, RNA and DNA binding proteins, functioning as competitive endogenous RNAs. The contribution of lncRNAs to microbial pathogenesis is largely neglected in eukaryotic pathogens despite the abundance of RNA sequencing datasets encompassing conditions of stress, gene deletions and conditions that mimic the host environment. The human fungal pathogen Cryptococcus neoformans encodes 6975 (84%) protein-coding and 1359 (16%) non-protein-coding RNAs, of which 1182 (14.2%) are lncRNAs defined by a threshold of greater than 200 nucleotides in length. Here, we discuss the current state of knowledge in C. neoformans lncRNA biology. Utilizing existing RNA seq datasets, we examine trends in lncRNA expression and discuss potential implications for pathogenesis.

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An Overview on Identification and Regulatory Mechanisms of Long Non-coding RNAs in Fungi

Cited by 15 publications

References 144 publications

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa

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

Long Non-Coding RNAs in Cryptococcus neoformans: Insights Into Fungal Pathogenesis

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