Histone deacetylation and cytosine methylation are required for the normal compartmentalization of heterochromatin in the genome organization of Neurospora crassa [Hi-C]

Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes: in the fungus Neurospora crassa, chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures that are anchored by heterochromatic region aggregates. However, insufficient information exists on how histone post-translational modifications, including acetylation, impact genome organization. In Neurospora, the HCHC (HDA-1, CDP-2, HP1, CHAP) complex deacetylates heterochromatic regions including centromeres: loss of individual HCHC members increases centromeric acetylation and cytosine methylation. Here, we evaluate the role of the HCHC complex on genome organization using chromosome conformation capture with high-throughput sequencing (Hi-C) in ?cdp-2 or ?chap deletion strains. CDP-2 loss increases interactions between intra- and inter-chromosomal heterochromatic regions, while removal of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different histone PTM patterns genome-wide: in Dcdp-2, heterochromatic H4K16 acetylation is increased, yet some heterochromatic regions lose H3K9 trimethylation, which locally increases inter-heterochromatin contacts; CHAP loss produces minimal acetylation changes but increases H3K9me3 enrichment in heterochromatin. Furthermore, deletion of the DIM-2 DNA methyltransferase in a ?cdp-2 background causes extensive genome disorder, as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how enhanced cytosine methylation ensures heterochromatic compartmentalization when silenced regions are acetylated. Overall design: We analyzed genome organization of mutants of a heterochromatin-specific histone deacetylase complex (the HCHC complex) found in the filamentous fungus Neurospora crassa by chromosome conformation capture by paired-end high-throughput sequencing (Hi-C); Hi-C libraries were generated with the four-base cutters DpnII and MseI, which monitor euchromatic and heterochromatic regions of the Neurospora genome, respectively, due to the location of the recognition sequences of these restriction enzymes. All HCHC mutant Hi-C data was compared to wild type Hi-C data, previously reported in Rodriguez et al. (Pubmed ID: 35244156). We also examined the histone post-translational modification enrichment of wild type and HCHC mutant strains, specifically looking at the acetylation of lysine 9 on histone H3, the acetylation of lysine 16 on histone H4, and the trimethylation of lysine 9 on histone H3.