Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë 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 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.

Transposable elements drive reorganisation of 3D chromatin during early embryogenesis

“…We find that strain-specific MERVL integrations, which are likely to have occurred more recently in evolutionary history, seem to occur preferentially at constitutive TAD boundaries. This is similar to observations made for other TE families, and is generally attributed to a preference to insert into open chromatin regions (Dixon et al 2012;Pope et al 2014;Darrow et al 2016;Giorgetti et al 2016;Winter et al 2018;de Jong et al 2014). On the other hand, MERVL shared between strains, which are likely to have occurred in a common ancestor and thus further back in evolutionary history, are not enriched at TAD boundaries, but can rather be found in a wide range of 3D contexts.…”

“…Mammalian genomes are characterised by the presence of a high amount of transposable elements (TEs) with increasingly recognized regulatory features for genome function such as transcription, splicing, and recombination, among others (Feschotte 2008;Bourque et al 2008;Friedli and Trono 2015;Thompson et al 2016). In recent years, TEs have also been associated with the three-dimensional organisation of chromatin in the nucleus, such as the inter-chromosomal colocalisation of similar repetitive elements (Cournac et al 2016), or the occurrence of TEs in domains or at domain boundaries (Dixon et al 2012;Pope et al 2014;Darrow et al 2016;Giorgetti et al 2016;Winter et al 2018). This is complemented by evidence for insulator function of specific TE families (Wang et al 2015;Schmidt et al 2012).…”

Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi

“…As with Ka values between conspecific strains (Figure 4b), the divergence of upstream regions is more pronounced when strains have different hosts (Figure 5b). Transposons are also increasingly recognized as key actors in regulating gene expression (Chuong, Elde, & Feschotte, 2017 (Winter et al, 2018). To exclude any possible effect of transposons on upstream genetic diversity, we excluded upstream regions that contain repeats and re-estimated genetic divergence; similar patterns were observed ( Figure S2).…”

“…Transposons are also increasingly recognized as key actors in regulating gene expression (Chuong, Elde, & Feschotte, ). In the maize genome, thousands of regulatory elements are derived from decayed transposon elements (H. Zhao et al, ), and repeat elements show similar, if less pronounced, regulatory effects in Epichloë (Winter et al, ). To exclude any possible effect of transposons on upstream genetic diversity, we excluded upstream regions that contain repeats and re‐estimated genetic divergence; similar patterns were observed (Figure ).…”

Analysis of Epichloë festucae small secreted proteins in the interaction with Lolium perenne

“…Deletion of key signaling genes results in the loss of this restricted growth and, in doing so, the ‘breakdown’ of the symbiosis [34-40]. Here, we make use of the fully assembled E. festucae genome [26] and EffectorP [41] to identify a suite of candidate effectors in this mutualistic endophyte, and analyse their genomic location to identify potential patterns of distribution. In addition, we use multiple transcriptome datasets to generate an expression profile for these candidate effectors, with the aim of identifying effectors with a potential role in the E. festucae - L. perenne interaction.…”