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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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:	Online
Language:	English
Published:	Oxford University Press 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797310/

id	pubmed-4797310
recordtype	oai_dc
spelling	pubmed-47973102016-03-21 Delineation of metabolic gene clusters in plant genomes by chromatin signatures 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 Genomics 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. Oxford University Press 2016-03-18 2016-02-18 /pmc/articles/PMC4797310/ /pubmed/26895889 http://dx.doi.org/10.1093/nar/gkw100 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ 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.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	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
spellingShingle	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 Delineation of metabolic gene clusters in plant genomes by chromatin signatures
author_facet	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
author_sort	Yu, Nan
title	Delineation of metabolic gene clusters in plant genomes by chromatin signatures
title_short	Delineation of metabolic gene clusters in plant genomes by chromatin signatures
title_full	Delineation of metabolic gene clusters in plant genomes by chromatin signatures
title_fullStr	Delineation of metabolic gene clusters in plant genomes by chromatin signatures
title_full_unstemmed	Delineation of metabolic gene clusters in plant genomes by chromatin signatures
title_sort	delineation of metabolic gene clusters in plant genomes by chromatin signatures
description	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.
publisher	Oxford University Press
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797310/
_version_	1613553866714906624

Delineation of metabolic gene clusters in plant genomes by chromatin signatures

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