Delineation of metabolic gene clusters in plant genomes by chromatin signatures

Nan Yu, Hans-Wilhelm Nuetzmann, James T MacDonald, Ben Moore, Ben Field, Souha Berriri, Martin Trick, Susan J Rosser, S Vinod Kumar, Paul S Freemont, Anne Osbourn

Research output: Contribution to journalArticlepeer-review

57 Citations (SciVal)


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.

Original languageEnglish
Pages (from-to)2255-2265
Number of pages11
JournalNucleic Acids Research
Issue number5
Early online date18 Feb 2016
Publication statusPublished - 18 Mar 2016


  • Arabidopsis
  • Arabidopsis Proteins
  • Avena
  • Chromatin
  • Chromosome Mapping
  • Gene Expression Regulation, Plant
  • Genome, Plant
  • High-Throughput Nucleotide Sequencing
  • Histones
  • Metabolic Networks and Pathways
  • Multigene Family
  • Plant Roots
  • Seedlings
  • Triterpenes
  • Zea mays
  • Journal Article
  • Research Support, Non-U.S. Gov't


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