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Delineation of metabolic gene clusters in plant genomes by chromatin signatures

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  • Nan Yu
  • Hans Wilhelm Nützmann
  • James T. Macdonald
  • Ben Moore
  • Ben Field
  • Souha Berriri
  • Martin Trick
  • Susan J. Rosser
  • S. Vinod Kumar
  • Paul S. Freemont
  • Anne Osbourn

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    Rights statement: The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Original languageEnglish
Article number100
Pages (from-to)2255-2265
Number of pages11
JournalNucleic Acids Research
Volume44
Issue number5
DOIs
Publication statusPublished - 18 Feb 2016

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.

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