ArticlePLoS genetics2018
Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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62 citing papers in PubMed, 128 citations in OpenAlex.
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- The 3D genome of Gigaspora margarita unveils stable chromatin and nucleolar organization and symbiont-dependent genome dynamics.The New phytologist · 2026Article
- Population-level Variability in Genome-wide Repressive Histone Marks in a Fungal Wheat Pathogen.Genome biology and evolution · 2026Article
- A Translocation within thebioRxiv : the preprint server for biology · 2026Article
- Organization principles of dynamic three-dimensional genome architecture associated with centromere clustering states.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Analysis of long-range contacts across cell types outlines a core sequence determinant of 3D genome organization.NAR genomics and bioinformatics · 2025Article
- Three-dimensional genome architecture connects chromatin structure and function in a major wheat pathogen.BMC biology · 2025Article
- The emerging sequence grammar of 3D genome organisation.Human genetics · 2025Review
- Genome Assembly, Polishing, and Analysis of the Chytrid Batrachochytrium salamandrivorans.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Identifying associations between short tandem repeat sequences and gene expression in yeast reveals specific repeated motifs encoding transcriptional regulatory proteins.Computational and structural biotechnology journal · 2025Article
- Unveiling an asymmetric plant-fungal symbiosis: morphological, cytogenetic, and molecular characterization of a haploidIMA fungus · 2025Article
- A constitutive heterochromatic region shapes genome organization and impacts gene expression in Neurospora crassa.BMC genomics · 2024Article
- A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression inbioRxiv : the preprint server for biology · 2024Article
- Article
- The jet-like chromatin structure defines active secondary metabolism in fungi.Nucleic acids research · 2024Article
- Strain-specific evolution and host-specific regulation of transposable elements in the model plant symbiont Rhizophagus irregularis.G3 (Bethesda, Md.) · 2024Article
- Genome Comparisons betweenJournal of fungi (Basel, Switzerland) · 2024Article
- Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen.Nature communications · 2024Article
- Meiosis in an asymmetric dikaryotic genome of Tremella fuciformis Tr01 facilitates new chromosome formation.Genome biology · 2023Review
- Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen.BMC biology · 2023Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. We use Hi-C data to examine the three-dimensional organisation of the genome, and RNA-seq data to investigate how Epichloë genome structure contributes to the suite of transcriptional changes needed to maintain symbiotic relationships with the grass host. Our results reveal a genome in which very repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences that are almost repeat-free. In contrast to other species reported to date, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.
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