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

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dc.contributor.author Hussey, Steven G.
dc.contributor.author Loots, Mattheus Theodor
dc.contributor.author Van der Merwe, Karen
dc.contributor.author Mizrachi, Eshchar
dc.contributor.author Myburg, Alexander Andrew
dc.date.accessioned 2017-08-11T06:17:47Z
dc.date.available 2017-08-11T06:17:47Z
dc.date.issued 2017-06-13
dc.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 ChIPseq 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. en_ZA
dc.description.department Forestry and Agricultural Biotechnology Institute (FABI) en_ZA
dc.description.department Genetics en_ZA
dc.description.department Plant Science en_ZA
dc.description.department Statistics en_ZA
dc.description.librarian am2017 en_ZA
dc.description.sponsorship The Department of Science and Technology (Strategic Grant for the Eucalyptus Genomics Platform), the National Research Foundation (Bioinformatics and Functional Genomics Programme Grant IUD 86936 and 97911), Incentive Funding Grant (AAM) (UID 8111), Mondi Ltd. and Sappi Ltd. en_ZA
dc.description.uri http://www.nature.com/srep en_ZA
dc.identifier.citation Hussey, S.G., Loots, M.T., Van der Merwe, K., Mizrachi, E. & Myburg, A.A. 2017, 'Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem', Scientific Reports, vol. 7, art. no. 3370, pp. 1-14. en_ZA
dc.identifier.issn 2045-2322 (online)
dc.identifier.other 10.1038/s41598-017-03665-1
dc.identifier.uri http://hdl.handle.net/2263/61623
dc.language.iso en en_ZA
dc.publisher Nature Publishing Group en_ZA
dc.rights © The Author(s) 2017. This article is licensed under a Creative Commons Attribution 4.0 International License. en_ZA
dc.subject Plants en_ZA
dc.subject Xylem development en_ZA
dc.subject RNA-seq en_ZA
dc.subject H3K27me3 en_ZA
dc.subject Xylogenesis en_ZA
dc.subject Genomic span en_ZA
dc.subject Histone modification en_ZA
dc.subject Secondary xylem en_ZA
dc.subject H3K4me3 en_ZA
dc.title Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem en_ZA
dc.type Article en_ZA


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