Fungal Pre-mRNA 3′-End Processing

Vavasseur, Aurélia; Shi, Yongsheng

doi:10.1007/978-3-319-05687-6_3

Cited by 3 publications

(6 citation statements)

References 167 publications

(277 reference statements)

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“…To search for cis-acting elements that may guide cleavage and polyadenylation, we extracted upstream 100 nt and downstream 100 nt sequence surrounding each PAS to examine nucleotide distributions and enriched motifs. Apparently, the single-nucleotide frequencies in F. graminearum are similar to that observed in yeasts (Vavasseur and Shi 2014;Liu et al 2017) (Fig. 7A).…”

Section: Polyadenylation Signals Surrounding Passsupporting

confidence: 76%

“…Pre-mRNA 3'-end processing have been studied extensively in yeasts and animals, but rarely in filamentous fungi (Vavasseur and Shi 2014;Tian and Manley 2017;Gruber and Zavolan 2019). APA plays important regulatory roles in virulence and development in M. oryzae (Franceschetti et al 2011).…”

Section: Discussionmentioning

confidence: 99%

“…Upon cis-acting elements surrounding the PASs, the 3'-end processing machinery also plays important roles in APA regulation by influencing PAS selections. This machinery includes three major complexes that are necessary for cleavage and polyadenylation in yeast: Cleavage Factor IA (CFIA), Cleavage Factor IB (CFIB), and Cleavage and Polyadenylation Factor (CPF) (Vavasseur and Shi 2014). We examined the expression of the orthologs of the core 3'-end processing factors from these complexes in F. graminearum.…”

Section: Regulatory Roles Of 3'-end Processing Factors In Pas Selectionmentioning

confidence: 99%

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Landscape, complexity and regulation of a filamentous fungal transcriptome

Lü

Chen

et al. 2021

Preprint

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Alternative splicing (AS) and alternative polyadenylation (APA) of pre-mRNAs contribute greatly to transcriptome complexity and gene expression regulation in higher eukaryotes. Their biological impact in filamentous fungi, however, has been poorly studied. Here we combine PacBio Isoform Sequencing and strand-specific RNA-Seq of multiple tissues together with mutant characterization to reveal the landscape, complexity and regulation of AS and APA in the filamentous plant pathogenic fungus Fusarium graminearum. We updated the reference genome and generated a comprehensive annotation comprising 51,617 transcript isoforms from 17,189 genes. Majority of the transcripts represent novel isoforms, including 2,998 undiscovered protein-coding genes. In total, 42.7% of multi-exonic genes and 64.8% of genes have AS and APA isoforms, respectively, suggesting AS and APA increase previously unrecognized transcriptome complexity in fungi. Nonsense-mediated mRNA decay factor FgUPF1 may not degrade AS transcripts with premature-stop codons but regulate ribosome biogenesis. Distal polyadenylation sites have a strong signal but proximal polyadenylation isoforms are high expressed. The core 3’-end processing factors FgRNA15, FgHRP1, and FgFIP1 play important roles in promoting proximal polyadenylation site usage and also intron splicing. Genome-wide increase in the abundance of transcripts with retained introns and long 3’-UTRs and downregulation of the spliceosomal and 3’-end processing factors are found in older tissues and quiescent conidia, indicating that intron retention and 3’-UTR lengthening may be a transcriptional signature of aging and dormancy in fungi. Overall, our study generates a comprehensive full-length transcript annotation for F. graminearum and provides new insights into the complexity and regulation of transcriptome in filamentous fungi.

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Section: Polyadenylation Signals Surrounding Passsupporting

confidence: 76%

Section: Discussionmentioning

confidence: 99%

Section: Regulatory Roles Of 3'-end Processing Factors In Pas Selectionmentioning

confidence: 99%

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Landscape, complexity and regulation of a filamentous fungal transcriptome

Lü

Chen

et al. 2021

Preprint

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“…Most of pre-mRNA 3′-end processing factors and polyadenylation signals of mammals and yeast have been identified and reviewed extensively ( 1 , 2 , 11 – 15 ). The polyadenylation machinery is a multi-subunit protein complex composed of ∼18 core proteins, although more than 80 proteins have been found to interact with pre-mRNA 3′-end processing components in humans ( 16 ).…”

Section: Introductionmentioning

confidence: 99%

“…By contrast, yeast poly(A) recognition signals diverge from mammalian polyadenylation signals despite sharing a tripartite poly(A) site recognition mechanism ( 13 ). Nevertheless, many yeast 3′ processing factors have counterparts in mammals, including Hrp1 for CFI m , CFIA (composed of Clp1, Pcf11, RNA14 and RNA15) for CstF and CFII (composed of Ydh1, Pta1, Yhh1 and Ysh1) for CPSF ( 15 ).…”

Section: Introductionmentioning

confidence: 99%

Multilayer regulatory mechanisms control cleavage factor I proteins in filamentous fungi

Rodríguez‐Romero

Franceschetti

Cendejas-Bueno

et al. 2014

Nucleic Acids Research

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Cleavage factor I (CFI) proteins are core components of the polyadenylation machinery that can regulate several steps of mRNA life cycle, including alternative polyadenylation, splicing, export and decay. Here, we describe the regulatory mechanisms that control two fungal CFI protein classes in Magnaporthe oryzae: Rbp35/CfI25 complex and Hrp1. Using mutational, genetic and biochemical studies we demonstrate that cellular concentration of CFI mRNAs is a limited indicator of their protein abundance. Our results suggest that several post-transcriptional mechanisms regulate Rbp35/CfI25 complex and Hrp1 in the rice blast fungus, some of which are also conserved in other ascomycetes. With respect to Rbp35, these include C-terminal processing, RGG-dependent localization and cleavage, C-terminal autoregulatory domain and regulation by an upstream open reading frame of Rbp35-dependent TOR signalling pathway. Our proteomic analyses suggest that Rbp35 regulates the levels of proteins involved in melanin and phenylpropanoids synthesis, among others. The drastic reduction of fungal CFI proteins in carbon-starved cells suggests that the pre-mRNA processing pathway is altered. Our findings uncover broad and multilayer regulatory mechanisms controlling fungal polyadenylation factors, which have profound implications in pre-mRNA maturation. This area of research offers new avenues for fungicide design by targeting fungal-specific proteins that globally affect thousands of mRNAs.

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Landscape and regulation of alternative splicing and alternative polyadenylation in a plant pathogenic fungus

Lü

Chen

et al. 2022

New Phytologist

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Summary Alternative splicing (AS) and alternative polyadenylation (APA) contribute significantly to the regulation of gene expression in higher eukaryotes. Their biological impact in filamentous fungi, however, is largely unknown. Here we combine PacBio Isoform‐Sequencing and strand‐specific RNA‐sequencing of multiple tissues and mutant characterization to reveal the landscape and regulation of AS and APA in Fusarium graminearum. We generated a transcript annotation comprising 51 617 isoforms from 17 189 genes. In total, 4997 and 11 133 genes are alternatively spliced and polyadenylated, respectively. Majority of the AS events alter coding sequences. Unexpectedly, the AS transcripts containing premature‐termination codons are not sensitive to nonsense‐mediated messenger RNA decay. Unlike in yeasts and animals, distal APA sites have strong signals, but proximal APA isoforms are highly expressed in F. graminearum. The 3′‐end processing factors FgRNA15, FgHRP1, and FgFIP1 play roles in promoting proximal APA site usage and intron splicing. A genome‐wide increase in intron inclusion and distal APA site usage and downregulation of the spliceosomal and 3′‐end processing factors were observed in older and quiescent tissues, indicating intron inclusion and 3′‐untranslated region lengthening as novel mechanisms in regulating aging and dormancy in fungi. This study provides new insights into the complexity and regulation of AS and APA in filamentous fungi.

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Fungal Pre-mRNA 3′-End Processing

Cited by 3 publications

References 167 publications

Landscape, complexity and regulation of a filamentous fungal transcriptome

Landscape, complexity and regulation of a filamentous fungal transcriptome

Multilayer regulatory mechanisms control cleavage factor I proteins in filamentous fungi

Landscape and regulation of alternative splicing and alternative polyadenylation in a plant pathogenic fungus

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