Loss of EZH2-like or SU(VAR)3\u20139-like proteins causes simultaneous perturbations in H3K27 and H3K9 tri-methylation and associated developmental defects in the fungus Podospora anserina

F Carlier,F Malagnac,L Maroc,R Debuchy,C Souaid,M Li,P Grognet,D Noordermeer

doi:10.1186/s13072-021-00395-7

Abstract

BackgroundSelective gene silencing is key to development. It is generally accepted that H3K27me3-enriched heterochromatin maintains transcriptional repression established during early development and regulates cell fate. Conversely, H3K9me3-enriched heterochromatin prevents differentiation but constitutes protection against transposable elements. We exploited the fungus Podospora anserina, a valuable alternative to higher eukaryote models, to question the biological relevance and functional interplay of these two distinct heterochromatin conformations.ResultsWe established genome-wide patterns of H3K27me3 and H3K9me3 modifications, and found these marks mutually exclusive within gene-rich regions but not within repeats. We generated the corresponding histone methyltransferase null mutants and showed an interdependence of H3K9me3 and H3K27me3 marks. Indeed, removal of the PaKmt6 EZH2-like enzyme resulted not only in loss of H3K27me3 but also in significant H3K9me3 reduction. Similarly, removal of PaKmt1 SU(VAR)3–9-like enzyme caused loss of H3K9me3 and substantial decrease of H3K27me3. Removal of the H3K9me binding protein PaHP1 provided further support to the notion that each type of heterochromatin requires the presence of the other. We also established that P. anserina developmental programs require H3K27me3-mediated silencing, since loss of the PaKmt6 EZH2-like enzyme caused severe defects in most aspects of the life cycle including growth, differentiation processes and sexual reproduction, whereas loss of the PaKmt1 SU(VAR)3–9-like enzyme resulted only in marginal defects, similar to loss of PaHP1.ConclusionsOur findings support a conserved function of the PRC2 complex in fungal development. However, we uncovered an intriguing evolutionary fluidity in the repressive histone deposition machinery, which challenges canonical definitions of constitutive and facultative heterochromatin.

Highlights

IntroductionIt is generally accepted that H3K27me3-enriched heterochromatin maintains transcriptional repression established during early development and regulates cell fate
Selective gene silencing is key to development
Further disruption of C. neoformans H3K9 methyltransferase Clr4 causes loss of both H3K9me2 and redistributed H3K27me3 modifications [41]. These findings suggest that co-factors, such as readers, are responsible for anchoring the H3K27 methyltransferase to its specific facultative heterochromatin compartments, that otherwise can be recruited to H3K9me constitutive heterochromatin, resulting in H3K9me/H3K27me co-occurrence

Summary

Introduction

It is generally accepted that H3K27me3-enriched heterochromatin maintains transcriptional repression established during early development and regulates cell fate. H3K9me3-enriched heterochromatin prevents differentiation but constitutes protection against transposable elements. Histones present in the compacted heterochromatin are enriched in either tri-methylated H3K27 (H3K27me3) or tri-methylated H3K9 (H3K9me3) [3]. The compact architecture of heterochromatin limits the accessibility of the transcription machinery to the embedded DNA, thereby silencing gene expression. Repeat-rich genomic regions enriched in H3K9me are referred to as ‘constitutive’ heterochromatin because the subsequent silencing may be constant across development [4]. The ‘facultative’ heterochromatin corresponds to the deposition of H3K27me on gene-rich regions, whose silencing is transient and dynamic across developmental processes, allowing cell type-specific differentiation and rapid adaptation of gene expression [5]

Results

Discussion

Conclusion