Integrating transposable elements in the 3D genome

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome.</p

A specialized metabolic network selectively modulates Arabidopsis root microbiota

Plant specialized metabolites have ecological functions, yet the presence of numerous uncharacterized biosynthetic genes in plant genomes suggests that many molecules remain unknown. We discovered a triterpene biosynthetic network in the roots of the small mustard plant Arabidopsis thaliana. Collectively, we have elucidated and reconstituted three divergent pathways for the biosynthesis of root triterpenes, namely thalianin (seven steps), thalianyl medium-chain fatty acid esters (three steps), and arabidin (five steps). A. thaliana mutants disrupted in the biosynthesis of these compounds have altered root microbiota. In vitro bioassays with purified compounds reveal selective growth modulation activities of pathway metabolites toward root microbiota members and their biochemical transformation and utilization by bacteria, supporting a role for this biosynthetic network in shaping an Arabidopsis-specific root microbial community

A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis

25 Pág.Plant specialized metabolites modulate developmental and ecological functions and comprise many therapeutic and other high-value compounds. However, the mechanisms determining their cell-specific expression remain unknown. Here we describe the transcriptional regulatory network that underlies cell-specific biosynthesis of triterpenes in Arabidopsis thaliana root tips. Expression of thalianol and marneral biosynthesis pathway genes depends on the phytohormone jasmonate and is limited to outer tissues. We show that this is promoted by the activity of redundant bHLH-type transcription factors from two distinct clades and coactivated by homeodomain factors. Conversely, the DOF-type transcription factor DAG1 and other regulators prevent expression of the triterpene pathway genes in inner tissues. We thus show how precise expression of triterpene biosynthesis genes is determined by a robust network of transactivators, coactivators and counteracting repressors.This Article was written in loving memory of A. Van Moerkercke (1979–2021). The authors thank A. Bleys for critically reading the manuscript; D. Gasperini for kindly sharing the ProMYCs:NLS-VENUS reporter lines, and P. Vittorioso for the dag1 mutant, ProDAG1:GUS and DAG1 over-expressing lines; J. R. Wendrich and T. Eekhout for assistance in the launching and analysis of the scRNAseq experiment; and S. Desmet and G. Goeminne from the VIB Metabolomics Core – Ghent for the thalianol profiling. This work was supported by the European Community’s Seventh Framework Program (FP7/2007–2013) under grant agreement 613692-TriForC and H2020 Program under grant agreement 760331-Newcotiana to A.G.; the Special Research Fund from Ghent University to A.G. and A.R. (project BOF18/GOA/013), and M.M. (project BOF20/GOA/012); the Flemish Government (AI Research program) to Y.S.; the Research Foundation Flanders with research project grants to A.G. (G004515N and G008417N) and a postdoctoral fellowship to P.F.-C.; a Swiss National Science Foundation postdoctoral fellowship (P300PA_177831) to M.C.; and a China Scholarship Council PhD scholarship to Y.B. A.O. acknowledges funding support from the John Innes Foundation and the BBSRC Institute Strategic Program Grant ‘Molecules from Nature – Products and Pathways’ (BBS/E/J/000PR9790).Peer reviewe

Delineation of metabolic gene clusters in plant genomes by chromatin signatures

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Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.Chemistry and Chemical Biolog

Gene clustering in plant specialized metabolism

Physically linked clusters of genes that encode the enzymatic information for the synthesis of specialized metabolites are a well-established feature of microbial secondary metabolism. In contrast, the biosynthesis of plant specialized metabolites has until recently been thought to be almost exclusively encoded by genes that are randomly scattered in the genome. However, recent reports highlight the growing number of examples of gene clusters for specialized metabolic pathways in plants. Numerous gene clusters that encode for the biosynthesis of different classes of metabolite have now been discovered in a variety of plant species. Comparison of these characterized clusters now enables us to begin to define their salient features and to exploit plant biosynthetic gene clusters for synthetic biology applications

Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana

The 3D genome is characterized by a complex organization made of genomic and epigenomic layers with profound implications on gene regulation and cell function. However, the understanding of the fundamental mechanisms driving the crosstalk between nuclear architecture and (epi)genomic information is still lacking. The plant Arabidopsis thaliana is a powerful model organism to address these questions owing to its compact genome for which we have a rich collection of microscopy, chromosome conformation capture (Hi-C) and ChIP-seq experiments. Using polymer modelling, we investigate the roles of nucleolus formation and epigenomics-driven interactions in shaping the 3D genome of A. thaliana. By validation of several predictions with published data, we demonstrate that self-attracting nucleolar organizing regions and repulsive constitutive heterochromatin are major mechanisms to regulate the organization of chromosomes. Simulations also suggest that interphase chromosomes maintain a partial structural memory of the V-shapes, typical of (sub)metacentric chromosomes in anaphase. Additionally, self-attraction between facultative heterochromatin regions facilitates the formation of Polycomb bodies hosting H3K27me3-enriched gene-clusters. Since nucleolus and heterochromatin are highly-conserved in eukaryotic cells, our findings pave the way for a comprehensive characterization of the generic principles that are likely to shape and regulate the 3D genome in many species.Funding: European Union’s H2020 Framework Programme through the ERC [609989 to M.A.M.-R.]; Spanish Ministry of Science and Innovation [BFU2017-85926-P to M.A.M.-R.]; Spanish Ministry of Science and Innovation to the EMBL [to C.R.G.]; Centro de Excelencia Severo Ochoa 2013–2017 [SEV-2012 0208]; CERCAProgramme/Generalitat de Catalunya, Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III; Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement; Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014–2020 Smart Growth Operating Program; Agence Nationale de la Recherche [ANR-18-CE12-0006-03, ANR-18-CE45-0022-01 to D.J.]; Royal Society [University Research Fellowship UF160138 to H.W.N.]; STSM Grant from COST Action CA17139. Funding for open access charge: COSTAction INC (CA18127), supported by COST(European Cooperation in Science and Technology

Emerging mechanistic insights into the regulation of specialized metabolism in plants

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A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis

Plant specialized metabolites modulate developmental and ecological functions and comprise many therapeutic and other high-value compounds. However, the mechanisms determining their cell-specific expression remain unknown. Here we describe the transcriptional regulatory network that underlies cell-specific biosynthesis of triterpenes in Arabidopsis thaliana root tips. Expression of thalianol and marneral biosynthesis pathway genes depends on the phytohormone jasmonate and is limited to outer tissues. We show that this is promoted by the activity of redundant bHLH-type transcription factors from two distinct clades and coactivated by homeodomain factors. Conversely, the DOF-type transcription factor DAG1 and other regulators prevent expression of the triterpene pathway genes in inner tissues. We thus show how precise expression of triterpene biosynthesis genes is determined by a robust network of transactivators, coactivators and counteracting repressors.</p