A gene graveyard in the genome of the fungus Podospora comata

Silar, Philippe; Dauget, Jean-Marc; Gautier, Valérie; Grognet, Pierre; Chablat, Michelle; Denmat, Sylvie Hermann‐Le; Couloux, Arnaud; Wincker, Patrick; Debuchy, Robert

doi:10.1007/s00438-018-1497-3

Cited by 20 publications

(47 citation statements)

References 43 publications

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“…This result is consistent with H3K27me3 being involved in regulation of gene expression during development programs since Pa_1_6263, which showed the most dramatic up-regulation effect (fold change > 25, p_value = 0.001 Fig. 5A), is supposed to be expressed during the sexual phase only (P. Silar et al 2019). Expression of genes encoding secondary metabolites (SM) is known to be sensitive to chromatin compaction (Gacek and Strauss 2012;Connolly, Smith, and Freitag 2013;Studt, Janevska, et al 2016;Studt, Rösler, et al 2016).…”

Section: Loss Of H3k27me3 In δPakmt6 Background Modifies Gene Expressionsupporting

confidence: 68%

“…RNA-seq experiments detected PaKmt6 transcripts of predicted structure in both vegetative mycelium and fruiting bodies (P. Silar et al 2019). However, while annotation of the PaKmt1 gene predicted that its ORF was made of two exons, RNA-seq experiments showed ambiguous profiles for PaKmt1 transcripts (P. Silar et al 2019). Dedicated reversetranscription polymerase chain reaction (RT-PCR) experiments revealed two distinct transcripts ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…By self-aggregation, chromo shadow domain containing proteins can bring together nucleosomes and thus condense the corresponding chromatin region (Canzio et al 2011). As for PaKmt6, RNA-seq data showed that the PaHP1 gene is expressed in both vegetative mycelium and fruiting bodies tissues (P. Silar et al 2019).…”

Section: H3k9me3 Reader Hp1 Is Present In P Anserinamentioning

confidence: 99%

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Loss of Polycomb Protein EZH2 causes major depletion of H3K27 and H3K9 tri-methylation and developmental defects in the fungusPodospora anserina

Carlier

Debuchy

Maroc

et al. 2020

Preprint

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Selective gene silencing is key to development. The H3K27me3 enriched heterochromatin maintains transcription repression established during early development and regulates cell fate. Conversely, H3K9me3 enriched heterochromatin prevents differentiation but constitutes a permanent protection against transposable element. We exploited the fungus Podospora anserina, a valuable alternative to higher eukaryote models to question the biological relevance and interplay of these two distinct heterochromatin conformations. We found that H3K27me3 and H3K9me3 modifications are mutually exclusive within gene-rich regions but not within repeats. Lack of PaKmt6 EZH2-like enzyme resulted in loss of H3K27me3 and in significant H3K9me3 reduction, whereas lack of PaKmt1 SU(VAR)3-9-like enzyme caused loss of H3K9me3 only. We established that P. anserina developmental programs require H3K27me3 mediated silencing unlike most fungi studied to date. Our findings provide new insight into roles of these histone marks and into the relationship between chromatin modifications and development.

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Section: Loss Of H3k27me3 In δPakmt6 Background Modifies Gene Expressionsupporting

confidence: 68%

Section: Resultsmentioning

confidence: 99%

Section: H3k9me3 Reader Hp1 Is Present In P Anserinamentioning

confidence: 99%

See 1 more Smart Citation

Loss of Polycomb Protein EZH2 causes major depletion of H3K27 and H3K9 tri-methylation and developmental defects in the fungusPodospora anserina

Carlier

Debuchy

Maroc

et al. 2020

Preprint

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“…Besides RT-PCR experiments (S1B Fig) indicated that PaRid transcripts could be detected up to T96 (96 hours post fertilization). Searching the available P. anserina RNA-seq data [36], we did not find any evidence of non-coding RNA at the PaRid locus (S1C Fig), as described for sense-antisense DmtA/tmdA transcripts found in A. nidulans [18].…”

Section: Resultsmentioning

confidence: 71%

“…See (Materials and methods section for details). (C) Coverage of RNA-seq mapped reads at the PaRid locus [36]. RNA-seq experiments were performed on RNA extracted from non-germinated ascospores (Ascospores), eight hours germinating ascospores (Germinated ascospores), 1-day- or 4-day-old mycelia, 2 days or 4 days post fertilization developing perithecia.…”

Section: Supporting Informationmentioning

confidence: 99%

A RID-like cytosine methyltransferase homologue controls sexual development in the fungusPodospora anserina

Grognet

Timpano

Carlier

et al. 2019

Preprint

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21DNA methyltransferases are ubiquitous enzymes conserved in bacteria, plants and 22 opisthokonta. These enzymes, which methylate cytosines, are involved in numerous 23 biological processes, notably development. In mammals and higher plants, methylation 24 patterns established and maintained by the cytosine DNA methyltransferases (DMTs) are 25 essential to zygotic development. In fungi, some members of an extensively conserved 26 fungal-specific DNA methyltransferase class are both mediators of the Repeat Induced Point 27 mutation (RIP) genome defense system and key players of sexual reproduction. Yet, no DNA 28 methyltransferase activity of these purified RID (RIP deficient) proteins could be detected in 29 vitro. These observations led us to explore how RID-like DNA methyltransferase encoding 30 genes would play a role during sexual development of fungi showing very little genomic DNA 31 methylation, if any. 32To do so, we used the model ascomycete fungus P. anserina. We identified the 33 PaRid gene, encoding a RID-like DNA methyltransferase and constructed knocked-out 34ΔPaRid defective mutants. Crosses involving P. anserina ΔPaRid mutants are sterile. Our 35 results show that, although gametes are readily formed and fertilization occurs in a ΔPaRid 36 background, sexual development is blocked just before the individualization of the dikaryotic 37 cells leading to meiocytes. Complementation of ΔPaRid mutants with ectopic alleles of 38 PaRid, including 39 demonstrated that the catalytic motif of the putative PaRid methyltransferase is essential to 40 ensure proper sexual development and that the expression of PaRid is spatially and 41 temporally restricted. A transcriptomic analysis performed on mutant crosses revealed an 42 overlap of the PaRid-controlled genetic network with the well-known mating-types gene 43 developmental pathway common to an important group of fungi, the Pezizomycotina. 44 45 46 3 Author Summary 47Sexual reproduction is considered to be essential for long-term persistence of 48 eukaryotic species. Sexual reproduction is controlled by strict mechanisms governing which 49 haploids can fuse (mating) and which developmental paths the resulting zygote will follow. In 50 mammals, differential genomic DNA methylation patterns of parental gametes, known as 51 'DNA methylation imprints' are essential to zygotic development, while in plants, global 52 genomic demethylation often results in female-sterility. Although animal and fungi are 53 evolutionary related, little is known about epigenetic regulation of gene expression and 54 development in multicellular fungi. Here, we report on a gene of the model fungus Podospora 55 anserina, encoding a protein called PaRid that looks like a DNA methyltrasferase. We 56 showed that expression of the catalytically functional version of the PaRid protein is required 57 in the maternal parental strain to form zygotes. By establishing the transcriptional profile of 58PaRid mutant strain, we identified a set of PaRid direct and/or indirect target genes. Half o...

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Phenotypic instability in fungi

Silar

2019

Advances in Applied Microbiology

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A gene graveyard in the genome of the fungus Podospora comata

Cited by 20 publications

References 43 publications

Loss of Polycomb Protein EZH2 causes major depletion of H3K27 and H3K9 tri-methylation and developmental defects in the fungusPodospora anserina

Loss of Polycomb Protein EZH2 causes major depletion of H3K27 and H3K9 tri-methylation and developmental defects in the fungusPodospora anserina

A RID-like cytosine methyltransferase homologue controls sexual development in the fungusPodospora anserina

Phenotypic instability in fungi

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