title: Delineation of metabolic gene clusters in plant genomes by chromatin signatures.
abstract: Plants are a tremendous source of diverse chemicals, including many natural product-derived drugs. It has recently become apparent that the genes for the biosynthesis of numerous different types of plant natural products are organized as metabolic gene clusters, thereby unveiling a highly unusual form of plant genome architecture and offering novel avenues for discovery and exploitation of plant specialized metabolism. Here we show that these clustered pathways are characterized by distinct chromatin signatures of histone 3 lysine trimethylation (H3K27me3) and histone 2 variant H2A.Z, associated with cluster repression and activation, respectively, and represent discrete windows of co-regulation in the genome. We further demonstrate that knowledge of these chromatin signatures along with chromatin mutants can be used to mine genomes for cluster discovery. The roles of H3K27me3 and H2A.Z in repression and activation of single genes in plants are well known. However, our discovery of highly localized operon-like co-regulated regions of chromatin modification is unprecedented in plants. Our findings raise intriguing parallels with groups of physically linked multi-gene complexes in animals and with clustered pathways for specialized metabolism in filamentous fungi.
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
authors.forename: Nan
authors.initials: N
authors.lastname: Yu
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK hans-wilhelm.nutzmann@jic.ac.uk.
authors.forename: Hans-Wilhelm
authors.initials: HW
authors.lastname: Nützmann
authors.affiliation: Centre for Synthetic Biology and Innovation, Imperial College, South Kensington Campus, London, SW7 2AZ, UK.
authors.forename: James T
authors.initials: JT
authors.lastname: MacDonald
authors.affiliation: Centre for Synthetic Biology and Innovation, Imperial College, South Kensington Campus, London, SW7 2AZ, UK.
authors.forename: Ben
authors.initials: B
authors.lastname: Moore
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
authors.forename: Ben
authors.initials: B
authors.lastname: Field
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
authors.forename: Souha
authors.initials: S
authors.lastname: Berriri
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Trick
authors.affiliation: School of Biological Sciences, University of Edinburgh, King's Building, Edinburgh, EH9 3JR, UK.
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Rosser
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
authors.forename: S Vinod
authors.initials: SV
authors.lastname: Kumar
authors.affiliation: Centre for Synthetic Biology and Innovation, Imperial College, South Kensington Campus, London, SW7 2AZ, UK.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Freemont
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK anne.osbourn@jic.ac.uk.
authors.forename: Anne
authors.initials: A
authors.lastname: Osbourn
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D018554:Avena / Q000235:genetics / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism; D002874:Chromosome Mapping; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D005810:Multigene Family; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D036226:Seedlings / Q000235:genetics / Q000378:metabolism; D014315:Triterpenes / Q000378:metabolism; D003313:Zea mays / Q000235:genetics / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D006657:Histones; D014315:Triterpenes; C548103:AT1G52740 protein, Arabidopsis; C521218:arabidiol; C531276:marneral; C528598:thalianol