Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem

Abstract Despite the considerable contribution of xylem development (xylogenesis) to plant biomass accumulation, its epigenetic regulation is poorly understood. Furthermore, the relative contributions of histone modifications to transcriptional regulation is not well studied in plants. We investigat...

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Autores principales: Steven G. Hussey, Mattheus T. Loots, Karen van der Merwe, Eshchar Mizrachi, Alexander A. Myburg
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Publicado: Nature Portfolio 2017
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Acceso en línea:https://doaj.org/article/e955c8de56924ed6831e8d2d668a9adb
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spelling oai:doaj.org-article:e955c8de56924ed6831e8d2d668a9adb2021-12-02T11:52:15ZIntegrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem10.1038/s41598-017-03665-12045-2322https://doaj.org/article/e955c8de56924ed6831e8d2d668a9adb2017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-03665-1https://doaj.org/toc/2045-2322Abstract Despite the considerable contribution of xylem development (xylogenesis) to plant biomass accumulation, its epigenetic regulation is poorly understood. Furthermore, the relative contributions of histone modifications to transcriptional regulation is not well studied in plants. We investigated the biological relevance of H3K4me3 and H3K27me3 in secondary xylem development using ChIP-seq and their association with transcript levels among other histone modifications in woody and herbaceous models. In developing secondary xylem of the woody model Eucalyptus grandis, H3K4me3 and H3K27me3 genomic spans were distinctly associated with xylogenesis-related processes, with (late) lignification pathways enriched for putative bivalent domains, but not early secondary cell wall polysaccharide deposition. H3K27me3-occupied genes, of which 753 (~31%) are novel targets, were enriched for transcriptional regulation and flower development and had significant preferential expression in roots. Linear regression models of the ChIP-seq profiles predicted ~50% of transcript abundance measured with strand-specific RNA-seq, confirmed in a parallel analysis in Arabidopsis where integration of seven additional histone modifications each contributed smaller proportions of unique information to the predictive models. This study uncovers the biological importance of histone modification antagonism and genomic span in xylogenesis and quantifies for the first time the relative correlations of histone modifications with transcript abundance in plants.Steven G. HusseyMattheus T. LootsKaren van der MerweEshchar MizrachiAlexander A. MyburgNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-14 (2017)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Steven G. Hussey
Mattheus T. Loots
Karen van der Merwe
Eshchar Mizrachi
Alexander A. Myburg
Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem
description Abstract Despite the considerable contribution of xylem development (xylogenesis) to plant biomass accumulation, its epigenetic regulation is poorly understood. Furthermore, the relative contributions of histone modifications to transcriptional regulation is not well studied in plants. We investigated the biological relevance of H3K4me3 and H3K27me3 in secondary xylem development using ChIP-seq and their association with transcript levels among other histone modifications in woody and herbaceous models. In developing secondary xylem of the woody model Eucalyptus grandis, H3K4me3 and H3K27me3 genomic spans were distinctly associated with xylogenesis-related processes, with (late) lignification pathways enriched for putative bivalent domains, but not early secondary cell wall polysaccharide deposition. H3K27me3-occupied genes, of which 753 (~31%) are novel targets, were enriched for transcriptional regulation and flower development and had significant preferential expression in roots. Linear regression models of the ChIP-seq profiles predicted ~50% of transcript abundance measured with strand-specific RNA-seq, confirmed in a parallel analysis in Arabidopsis where integration of seven additional histone modifications each contributed smaller proportions of unique information to the predictive models. This study uncovers the biological importance of histone modification antagonism and genomic span in xylogenesis and quantifies for the first time the relative correlations of histone modifications with transcript abundance in plants.
format article
author Steven G. Hussey
Mattheus T. Loots
Karen van der Merwe
Eshchar Mizrachi
Alexander A. Myburg
author_facet Steven G. Hussey
Mattheus T. Loots
Karen van der Merwe
Eshchar Mizrachi
Alexander A. Myburg
author_sort Steven G. Hussey
title Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem
title_short Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem
title_full Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem
title_fullStr Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem
title_full_unstemmed Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem
title_sort integrated analysis and transcript abundance modelling of h3k4me3 and h3k27me3 in developing secondary xylem
publisher Nature Portfolio
publishDate 2017
url https://doaj.org/article/e955c8de56924ed6831e8d2d668a9adb
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