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

Abstract

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.

Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization

“…In Lmb, having more than 30% of TE, 33% of the genome is associated with H3K9me3 while the genome of Lml, having a low TE content, shows a low enrichment in H3K9me3 (4% of H3K9me3). Domains enriched with H3K4me2 and domains enriched with H3K9me3 are mutually exclusive in the genomes of Lmb and Lml, as was shown in Neurospora crassa, Fusarium fujikuroi, Z. tritici or P. anserina (Smith et al 2008;Jamieson et al 2013;Wiemann et al 2013;Schotanus et al 2015;Carlier et al 2020). H3K27me3 has been detected in most filamentous fungi investigated so far, except in Mucor, Rhizopus or Aspergilli such as Aspergillus nidulans (Gacek-Matthews et al 2016;reviewed in Freitag 2017).…”

“…Gene-rich regions are enriched with H3K4me2 and H3K27me3, while TE-rich regions are associated with H3K9me3. The proportion of H3K9me3 in a genome often reflects the TE content, as was described in Z. tritici or Podospora anserina (Schotanus et al 2015;Carlier et al 2020). In Lmb, having more than 30% of TE, 33% of the genome is associated with H3K9me3 while the genome of Lml, having a low TE content, shows a low enrichment in H3K9me3 (4% of H3K9me3).…”

Combinations of maternal-specific repressive epigenetic marks in the endosperm control seed dormancy

“…The combined presence of H3K27me3 with the heterochromatic modification H3K9me3 was also reported to occur on TEs and repeat-rich regions in the protozoa Tetrahymena and Paramecium (Frapporti et al, 2019; Liu et al, 2007; Zhao et al, 2019) and the fungus Podospora anserine (Carlier et al, 2020). In Podospora anserine , the presence of double repressive modifications is restricted to TEs and repeat-rich regions, while H3K27me3 alone is located in genic regions; indicating a similar molecular distinction of constitutively silenced regions marked by double modifications from regions that require activation during specific developmental stages marked by H3K27me3 alone.…”

Combinations of maternal-specific repressive epigenetic marks in the endosperm control seed dormancy

“…The combined presence of H3K27me3 with the heterochromatic modification H3K9me3 was also reported to occur on TEs and repeat-rich regions in the protozoa Tetrahymena and Paramecium ( Frapporti et al, 2019 ; Liu et al, 2007 ; Zhao et al, 2019 ) and the fungus Podospora anserine ( Carlier et al, 2020 ). In P. anserine , the presence of double repressive modifications is restricted to TEs and repeat-rich regions, while H3K27me3 alone is located in genic regions, indicating a similar molecular distinction of constitutively silenced regions marked by double modifications from regions that require activation during specific developmental stages marked by H3K27me3 alone.…”

“…The establishment of H3K9me2 in Arabidopsis depends on the SU(VAR)3–9 homologous proteins (SUVHs), KRYPTONITE (or SUVH4), SUVH5 and SUVH6 that act in a feedback loop with CHG methylation (CHGm) established by the CHROMOMETHYLTRANSFERASE 3 (CMT3) ( Kenchanmane Raju et al, 2019 ; Zhang et al, 2018 ). In animals and plants, H3K27me3 and H3K9me2 are generally exclusive repressive marks ( Wiles and Selker, 2017 ); however, they co-occur in certain tissue types like the plant endosperm ( Klosinska et al, 2016 ; Moreno-Romero et al, 2016 ; Weinhofer et al, 2010 ), as well as in specific organisms as filamentous fungi and bryophytes ( Carlier et al, 2020 ; Montgomery et al, 2020 ). Furthermore, redistribution of H3K27me3 to heterochromatic regions occurs when constitutive heterochromatin is disrupted, indicating that specific features of heterochromatin prevent PRC2 recruitment ( Deleris et al, 2012 ; Jamieson et al, 2016 ; Peters et al, 2003 ; Wiles and Selker, 2017 ).…”