The genome organization of Neurospora crassa at high resolution uncovers principles of fungal chromosome topology

Abstract

The eukaryotic genome must be precisely organized for its proper function, as genome topology impacts transcriptional regulation, cell division, replication, and repair, among other essential processes. Disruptions to human genome topology can lead to diseases, including cancer. The advent of chromosome conformation capture with high-throughput sequencing (Hi-C) to assess genome organization has revolutionized the study of nuclear genome topology; Hi-C has elucidated numerous genomic structures, including chromosomal territories, active/silent chromatin compartments, Topologically Associated Domains, and chromatin loops. While low-resolution heatmaps can provide important insights into chromosomal level contacts, high resolution Hi-C datasets are required to reveal folding principles of individual genes. Of particular interest are high-resolution chromosome conformation datasets of organisms modeling the human genome. Here, we report the genome topology of the fungal model organism Neurospora crassa at a high resolution. Our composite Hi-C dataset, which merges two independent datasets generated with restriction enzymes that monitor euchromatin (DpnII) and heterochromatin (MseI), along with our DpnII/MseI double digest dataset, provide exquisite detail for both the conformation of entire chromosomes and the folding of chromatin at the resolution of individual genes. Within constitutive heterochromatin, we observe strong yet stochastic internal contacts, while euchromatin enriched with either activating or repressive histone post-translational modifications associates with constitutive heterochromatic regions, suggesting inter-compartment contacts form to regulate transcription. Consistent with this, a strain with compromised heterochromatin experiences numerous changes in gene expression. Our high-resolution Neurospora Hi-C datasets are outstanding resources to the fungal community and provide valuable insights into higher organism genome topology.

Lineage-specific genes are clustered with allorecognition loci and respond to G × E factors regulating the switch from asexual to sexual reproduction inNeurospora

“…However, orphan- het gene clusters and their neighbor genes were syntenic mainly within very closely related taxa, and many orphan genes exhibited no expression under common laboratory settings—even across a range of nutrient conditions and developmental stages. Interestingly, heterochromatic interactions of intra- and inter-telomeric contacts were reported as common in N. crassa (Rodriguez et al 2022), implying potential cis- and trans- regulation at chromosomal level of expression integration in these orphan-gene enriched regions. It is possible that integrating orphan- het gene clusters into existing regulatory systems temporally and spatially modifies the original functions that are expected only under common growth conditions.…”

Visual integration of omics data to improve 3D models of fungal chromosomes

“…Initially limited to the context of viewing biomolecules (nanoscale), visualization software was thus extended to representation of the 3D organization of chromosomes at the mesoscale. Surprisingly, recent Hi-C studies on S. cerevisiae, S. pombe and N. crassa do not feature 3D models (Rodriguez et al 2022;Tanizawa et al 2017;Costantino et al 2020). In a context where i) an increasing number of Hi-C studies are generated, ii) methods for 3D modeling of Hi-C contacts exist and iii) software for 3D visualization is routinely available in structural biology, one may wonder why contact maps are not associated with 3D models more often.…”

“…In 2016, Galazka et al (Galazka et al 2016) identified an inversion of the contig named "12.304", corresponding to a large region in chromosome 6. In 2022, Rodriguez et al (Rodriguez et al 2022) further improved the original assembly "nc12" based on Hi-C data analysis. The updated assembly that integrates the improvements of Galazka et al and Rodriguez et al is available in the GEO database under the accession "assembly nc14".…”

“…Those territories are another well described example of the functional importance of chromatin structure and are observed in many different organisms. Well known in yeasts, chromosome territories are still debated in N. crassa (Rodriguez et al 2022).…”

“…In this study, we are specifically interested in seeing the spatial organization of fungal chromosomes. Our laboratory has long-standing expertise in functional genomics projects in yeasts (Denecker et al 2020; Poinsignon et al 2022; Sénécaut et al 2022) or filamentous fungi (Grognet et al 2019; Carlier et al 2021; Lelandais et al 2022), and spatial genome organization in fungi has already been investigated, for model species like Saccharomyces cerevisiae (Duan et al 2010; Tokuda et al 2012), Schizosaccharomyces pombe (Grand et al 2014; Tanizawa et al 2010; Gallardo et al 2019; Noma 2017) and Neurospora crassa (Galazka et al 2016; Rodriguez et al 2022). Notably, the nuclear architecture of N. crassa , a multicellular fungus that grows as a mycelium with a network of hyphae (Galagan et al 2003), has structural homology (thanks to the existence of heterochromatin and euchromatin) with the human genome (Rodriguez et al 2022).…”