Delineation of metabolic gene clusters in plant genomes by chromatin signatures

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 fo...

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Bibliographic Details
Published in:Nucleic acids research 2016-03, Vol.44 (5), p.2255-2265
Main Authors: Yu, Nan, Nützmann, Hans-Wilhelm, MacDonald, James T, Moore, Ben, Field, Ben, Berriri, Souha, Trick, Martin, Rosser, Susan J, Kumar, S Vinod, Freemont, Paul S, Osbourn, Anne
Format: Article
Language:English
Subjects:
Arabidopsis - genetics
Arabidopsis - metabolism
Arabidopsis Proteins - genetics
Arabidopsis Proteins - metabolism
Avena - genetics
Avena - metabolism
Chromatin - chemistry
Chromatin - metabolism
Chromosome Mapping
Gene Expression Regulation, Plant
Genome, Plant
Genomics
High-Throughput Nucleotide Sequencing
Histones - genetics
Histones - metabolism
Life Sciences
Metabolic Networks and Pathways
Multigene Family
Plant Roots - genetics
Plant Roots - metabolism
Seedlings - genetics
Seedlings - metabolism
Triterpenes - metabolism
Zea mays - genetics
Zea mays - metabolism
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkw100