Nuclear genome organization in fungi: from gene folding to Rabl chromosomes

Abstract

Comparative genomics has recently provided unprecedented insights into the biology and evolution of the fungal lineage. In the post-genomics era, a major research interest focuses now on detailing the functions of fungal genomes, i.e. how genomic information manifests into complex phenotypes. Emerging evidence across diverse eukaryotes has revealed that the organization of DNA within the nucleus is critically important. Here, we discuss the current knowledge on the fungal genome organization, from the association of chromosomes within the nucleus to topological structures at individual genes and the genetic factors required for this hierarchical organization. Chromosome conformation capture followed by high-throughput sequencing (Hi-C) has elucidated how fungal genomes are globally organized in Rabl configuration, in which centromere or telomere bundles are associated with opposite faces of the nuclear envelope. Further, fungal genomes are regionally organized into Topologically Associated Domain-like (TAD-like) chromatin structures. We discuss how chromatin organization impacts the proper function of DNA-templated processes across the fungal genome. Nevertheless, this view is limited to a few fungal taxa given the paucity of fungal Hi-C experiments. We advocate for exploring genome organization across diverse fungal lineages to ensure the future understanding of the impact of nuclear organization on fungal genome function.

Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization ofNeurospora crassa

“…The genome of the wild type (WT) Neurospora crassa strain N150 (74-OR23-IVA [Fungal Genetic Stock Center #2489]) is organized by heterochromatin aggregates, which form TAD-like structures (Figure 1A) (16, 26–28). Heterochromatic regions in Neurospora depend on the HDAC HCHC for deacetylation of histone tails, transcriptional silencing, and a normal 5 m C distribution (40).…”

“…A plot of the interactions between LG II and LG III in Δ chap shows the paucity of inter-chromosomal constitutive heterochromatic contacts (Figure S11A), which is highlighted when comparing WT and Δ chap Mse I Hi-C data (Figure 2B). The decrease in heterochromatin bundling compromises the inter-chromosomal arm interactions characteristic of the Rabl conformation (28), as reduced euchromatin interactions across the left and right chromosomal arms are evident in a WT and Δ chap Dpn II Hi-C comparison (Figure S10B). Quantification of the strongest inter-chromosomal interaction gains between histone PTM-enriched bins in a Δ cdp-2 Mse I dataset, relative to WT, shows 81.5% of H3K9me3 enriched bins gain interactions, but few H3K9me3-enriched bins gain strong contacts with bins enriched with euchromatic marks, such as H3K27ac (Figure 2C, left).…”

“…Here, heterochromatin hyperacetylation in a Δ cdp-2 strain causes increased contact probability within heterochromatic loci, as well as between distant intra– and inter-chromosomal heterochromatic regions, while CHAP loss reduces heterochromatin aggregation without strong histone acetylation changes. Neither gene deletion abolished the Rabl chromosome conformation typical of fungal genomes (28), suggesting the overall genome organization can still form despite HCHC loss. Together, our data suggest that CDP-2 and CHAP have distinct functions in the HCHC complex that differentially impact genome organization.…”

“…Neurospora chromosomes (“Linkage Groups” [LG]) form TAD-like structures, also known as “Regional Globule Clusters”, in which the heterochromatic regions flanking euchromatin aggregate, forming loops that cluster several euchromatic globules together in an uninsulated manner (16, 26, 27). However, as opposed to the robust chromosome territories in metazoans (1, 22, 24, 25), fungal chromosomes form a Rabl conformation, in which centromeres bundle independently from telomere clusters at the nuclear periphery (16, 26–28, 43), as directly observed in Neurospora (26–28); this Rabl structure allows for weak chromosome territories with extensive inter-chromosomal contacts.…”

“…Filamentous fungi, like Neurospora crassa , are excellent model organisms for understanding eukaryotic genome organization (16, 26–28). The predominantly haploid Neurospora genome, typical among fungi, is small (4.1 x 10 7 bp) (29), which allows for cost-efficient genomic sequencing experiments.…”