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.
