Normal Patterns of Histone H3K27 Methylation Require the Histone Variant H2A.Z inNeurospora crassa

Abstract

<jats:p><jats:italic>Neurospora crassa</jats:italic> contains a minimal Polycomb repression system, which provides rich opportunities to explore Polycomb-mediated repression across eukaryotes and enables genetic studies that can be difficult in plant and animal systems. Polycomb Repressive Complex 2 is a multi-subunit complex that deposits mono-, di-, and tri-methyl groups on lysine 27 of histone H3, and tri-methyl H3K27 is a molecular marker of transcriptionally repressed facultative heterochromatin. In mouse embryonic stem cells and multiple plant species, H2A.Z has been found to be co-localized with H3K27 methylation. H2A.Z is required for normal H3K27 methylation in these experimental systems, though the regulatory mechanisms are not well understood. We report here that <jats:italic>Neurospora crassa</jats:italic> mutants lacking H2A.Z or SWR-1, the ATP-dependent histone variant exchanger, exhibit a striking reduction in levels of H3K27 methylation. RNA-sequencing revealed downregulation of <jats:italic>eed, </jats:italic>encoding a subunit of PRC2, in an <jats:italic>hH2Az</jats:italic> mutant compared to wild type and overexpression of EED in a ∆<jats:italic>hH2Az</jats:italic>;∆<jats:italic>eed</jats:italic> background restored most H3K27 methylation. Reduced <jats:italic>eed</jats:italic> expression leads to region-specific losses of H3K27 methylation suggesting differential dependence on EED concentration is critical for normal H3K27 methylation at certain regions in the genome.</jats:p>

Effect of H2A.Z deletion is rescued by compensatory mutations in Fusarium graminearum

“…graminearum ’s genome, including genes involved in secondary metabolism [ 51 ]. However, regarding the function of H2A.Z in fungi, very few studies were carried out in Neurospora crassa studying specifically the function of H2A.Z and identifying a role in oxidative stress response [ 52 , 53 ] as well as a link with the deposition of H3K27me3 [ 54 ].…”

Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin

“…H2A.Z is reported to promote chromatin accessibility in in embryonic stem cells [ 60 ]⁠⁠. We compared previously published H2A.Z ChIP-seq data [ 22 ] to our ATAC-seq data and found that H2A.Z was enriched flanking most, but not all ACRs (e.g. see Cluster 3).…”

“…To quantify the level of accessibility in heterochromatin and euchromatin, we used bedtools intersect to determine the number of ACRs that overlap with H3K27me2/3 or H3K9me3 (Table S3 ). H3K27me2/3 is enriched in 309 domains covering 6% of the genome [ 22 ]⁠. We identified 68/7132 ACRs that overlap with called H3K27me2/3 enriched regions.…”

“…Antiflag ChIP was performed as described above. Previously published data for H3K36me2 in the Δset-2 mutant, [50], hH2Az-GFP [22], and WC-2, [57] were re-mapped to the current Neurospora genome assembly and analyzed as described above.…”

“…Conversely, heterochromatin is transcriptionally repressed and marked by histone H3 lysine 9 methylation (H3K9me3) [6][7][8][9][10] or histone H3 lysine 27 methylation (H3K27me2/ 3) [6,[11][12][13][14][15][16]. Chromatin environments can also be defined by the presence of histone variants such as histone H2A.Z, which is found surrounding transcriptional start sites and within vertebrate and plant enhancers [17][18][19][20][21][22][23].…”