Global identification of alternative splicing in Shiraia bambusicola and analysis of its regulation in hypocrellin biosynthesis

Liu, Xinyao; Fan, Li; Gao, Jian; Shen, Xiaoye; Hou, Cheng‐Lin

doi:10.1007/s00253-019-10189-3

Cited by 11 publications

(5 citation statements)

References 55 publications

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“…However, this later estimation is based on ESTs and might underestimate the real number of ASEs [21]. Indeed, recent RNA-seq showed ASEs in 24% of expressed genes in an oomycete [53] and 38% in a plant pathogenic ascomycete [54]. One IR event was recently evidenced for the PaKmt1 gene [26].…”

Section: Discussionmentioning

confidence: 99%

New insights into genome annotation in Podospora anserina through re-exploiting multiple RNA-seq data

et al. 2022

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Background Publicly available RNA-seq datasets are often underused although being helpful to improve functional annotation of eukaryotic genomes. This is especially true for filamentous fungi genomes which structure differs from most well annotated yeast genomes. Podospora anserina is a filamentous fungal model, which genome has been sequenced and annotated in 2008. Still, the current annotation lacks information about cis-regulatory elements, including promoters, transcription starting sites and terminators, which are instrumental to integrate epigenomic features into global gene regulation strategies. Results Here we took advantage of 37 RNA-seq experiments that were obtained in contrasted developmental and physiological conditions, to complete the functional annotation of P. anserina genome. Out of the 10,800 previously annotated genes, 5’UTR and 3’UTR were defined for 7554, among which, 3328 showed differential transcriptional signal starts and/or transcriptional end sites. In addition, alternative splicing events were detected for 2350 genes, mostly due alternative 3’splice sites and 1732 novel transcriptionally active regions (nTARs) in unannotated regions were identified. Conclusions Our study provides a comprehensive genome-wide functional annotation of P. anserina genome, including chromatin features, cis-acting elements such as UTRs, alternative splicing events and transcription of non-coding regions. These new findings will likely improve our understanding of gene regulation strategies in compact genomes, such as those of filamentous fungi. Characterization of alternative transcripts and nTARs paves the way to the discovery of putative new genes, alternative peptides or regulatory non-coding RNAs.

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Section: Discussionmentioning

confidence: 99%

New insights into genome annotation in Podospora anserina through re-exploiting multiple RNA-seq data

et al. 2022

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“…AS events in fungi play a role in growth, response to environmental stress, and pathogenicity [39]. For example, in S. bambusicola, AS events regulate biological processes, including pigment synthesis [40]. In comparison group A_vs._B, AS-related genes were primarily enriched in the ribosome, TCA cycle, and oxidative phosphorylation pathways.…”

Section: Discussionmentioning

confidence: 99%

Metabolic Regulation of Two pksCT Gene Transcripts in Monascus ruber Impacts Citrinin Biosynthesis

He,

Zhu,

Dong

et al. 2023

JoF

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Citrinin (CIT), a secondary metabolite produced by the filamentous fungi Monascus species, exhibits nephrotoxic, hepatotoxic, and carcinogenic effects in mammals, remarkably restricting the utilization of Monascus-derived products. CIT synthesis is mediated through the pksCT gene and modified by multiple genetic factors. Here, the regulatory effects of two pksCT transcripts, pksCTα, and pksCTβ, generated via pre-mRNA alternative splicing (AS), were investigated using hairpin RNA (ihpRNA) interference, and their impact on CIT biosynthesis and the underlying mechanisms were assessed through chemical biology and transcriptome analyses. The CIT yield in ihpRNA-pksCTα and ihpRNA-pksCT (α + β) transformants decreased from 7.2 μg/mL in the wild-type strain to 3.8 μg/mL and 0.08 μg/mL, respectively. Notably, several genes in the CIT biosynthetic gene cluster, specifically mrl3, mrl5, mrr1, and mrr5 in the ihpRNA-pksCT (α + β) transformant, were downregulated. Transcriptome results revealed that silencing pksCT has a great impact on carbohydrate metabolism, amino acid metabolism, lipid metabolism, and AS events. The key enzymes in the citrate cycle (TCA cycle) and glycolysis were significantly inhibited in the transformants, leading to a decrease in the production of biosynthetic precursors, such as acetyl-coenzyme-A (acetyl-coA) and malonyl-coenzyme-A (malonyl-coA). Furthermore, the reduction of CIT has a regulatory effect on lipid metabolism via redirecting acetyl-coA from CIT biosynthesis towards lipid biosynthesis. These findings offer insights into the mechanisms underlying CIT biosynthesis and AS in Monascus, thus providing a foundation for future research.

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“…However, this later estimation is based on ESTs and might underestimate the real number of ASEs (21). Indeed, recent RNA-seq showed ASEs in 24% of expressed genes in an oomycete (51) and 38% in a plant pathogenic ascomycete (52). One IR event was recently evidenced for the PaKmt1 gene (26).…”

Section: Discussionmentioning

confidence: 99%

Re-exploiting multiple RNA-seq data to identify transcript variations in Podospora anserina

Lelandais

Remy

Malagnac

et al. 2022

Preprint

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Publicly available RNA-seq datasets are often underused although being helpful to improve functional annotation of eukaryotic genomes. This is especially true for filamentous fungi genomes which structure differs from most well annotated yeast genomes. Podospora anserina is a filamentous fungal model, which genome has been sequenced and annotated in 2008. Still, the current annotation lacks information about cis-regulatory elements, including promoters, transcription starting sites and terminators, which are instrumental to integrate epigenomic features into global gene regulation strategies. Here we took advantage of 37 RNA-seq experiments that were obtained in contrasted developmental and physiological conditions, to complete the functional annotation of P. anserina genome. Out of the 10,800 previously annotated genes, 5'UTR and 3'UTR were defined for 7,554, among which, 3,328 showed differential transcriptional signal starts and/or transcriptional end sites. In addition, alternative splicing events were detected for 2350 genes, mostly due alternative 3'splice site and 1,958 novel transcriptionally active regions (nTARs) in unannotated regions were identified. Our study provides a comprehensive genome-wide functional annotation release of P. anserina genome, including chromatin features, cis-acting elements such as UTRs, alternative splicing events and transcription of non-coding regions. These new findings will likely improve our understanding of gene regulation strategies in compact genomes, such as those of filamentous fungi. Characterization of alternative transcripts and nTARs paves the way to the discovery of putative new genes, alternative peptides or regulatory non-coding RNAs.

show abstract

Global identification of alternative splicing in Shiraia bambusicola and analysis of its regulation in hypocrellin biosynthesis

Cited by 11 publications

References 55 publications

New insights into genome annotation in Podospora anserina through re-exploiting multiple RNA-seq data

New insights into genome annotation in Podospora anserina through re-exploiting multiple RNA-seq data

Metabolic Regulation of Two pksCT Gene Transcripts in Monascus ruber Impacts Citrinin Biosynthesis

Re-exploiting multiple RNA-seq data to identify transcript variations in Podospora anserina

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