Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungusEpichloë festucae

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 organization 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. Coupling it with RNAseq and HiC data, we investigate how the structure of the genome contributes to the suite of transcriptional changes that an Epichloë species needs to maintain symbiotic relationships with its grass host. Our results reveal a unique "patchwork" genome, in which repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences. In contrast to other species, 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.A total of 6,709 base-level errors, mostly single base indels (96.9%), were polished using the Pilon finisher with 87x coverage Illumina paired-end sequencing as input. Finally, telomeres were trimmed to the nearest canonical sequence and, where necessary, chromosome sequences were reverse-complemented to place the short arm of the chromosome first by

Regulation of subtelomeric fungal secondary metabolite genes by H3K4me3 regulators CclA and KdmB

“…The EAS and LTM clusters in Epichloë festucae strain Fl1 (Ascomycota, Clavicipitaceae) are located immediately adjacent to the telomeres on the long arms of chromosome I and III, respectively (Winter et al , ), and encode genes for the biosynthesis of ergot alkaloids and indole diterpenes (Young et al , ; Fleetwood et al , ; Schardl et al , ). The telomere proximal genes of these clusters, lpsB ( EAS cluster) and ltmE ( LTM cluster) are located 7 and 11 kb from the telomeres, respectively, while the entire clusters of 11 genes extend up to 90 kb from the telomeres (Schardl et al , ; Winter et al , ). E. festucae is a symbiont of Lolium perenne (perennial ryegrass), and colonizes the intercellular spaces of the host aerial tissues (Scott et al , ).…”

“…E. festucae is a symbiont of Lolium perenne (perennial ryegrass), and colonizes the intercellular spaces of the host aerial tissues (Scott et al , ). Remarkably, the eas and ltm genes undergo two extremes of transcriptional regulation; from a silent state in axenic culture, to a fully activated state in planta (Young et al , ), where the ltm genes are among the most highly expressed genes (Winter et al , ). These attributes make the EAS and LTM clusters particularly suited for the study of subtelomeric gene regulation.…”