Identification and functional evaluation of accessible chromatin associated with wood formation in Eucalyptus grandis

Abstract

Accessible chromatin changes dynamically during development and harbours functional regulatory regions which are poorly understood in the context of wood development. We explored the importance of accessible chromatin in Eucalyptus grandis in immature xylem generally, and MYB transcription factor-mediated transcriptional programmes specifically.We identified biologically reproducible DNase I Hypersensitive Sites (DHSs) and assessed their functional significance in immature xylem through their associations with gene expression, epigenomic data and DNA sequence conservation. We identified in vitro DNA binding sites for six secondary cell wall-associated Eucalyptus MYB (EgrMYB) transcription factors using DAP-seq, reconstructed protein-DNA networks of predicted targets based on binding sites within or outside DHSs and assessed biological enrichment of these networks with published datasets.25 319 identified immature xylem DHSs were associated with increased transcription and significantly enriched for various epigenetic signatures (H3K4me3, H3K27me3, RNA pol II), conserved noncoding sequences and depleted single nucleotide variants. Predicted networks built from EgrMYB binding sites located in accessible chromatin were significantly enriched for systems biology datasets relevant to wood formation, whereas those occurring in inaccessible chromatin were not.Our study demonstrates that DHSs in E. grandis immature xylem, most of which are intergenic, are of functional significance to gene regulation in this tissue.

Allele‐specific expression and chromatin accessibility contribute to heterosis in tea plants (Camellia sinensis)

“…Chromatin accessibility reflects the role of chromatin in the regulation of gene expression. Different transcriptional co‐regulators can combine with dynamic chromatin accessibility and confer specific responses and regulations to plant developmental and environmental signals at the molecular level (Brown et al., 2019; Maher et al., 2017; Potter et al., 2018; Wang, et al., 2021a; Wilkins et al., 2016). Several methods based on the sensitivity of non‐specific nuclease cleavage are applied to identify accessible chromatin regions (ACRs; Zentner & Henikoff, 2014).…”

Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML

“…In previous work, we observed that putative target genes linked to SCW-related EgrMYB DAP-seq binding sites located in open chromatin were overrepresented in systems biology datasets linked to wood formation biology, while those found outside of accessible chromatin were not (Brown et al 2019). This suggests that true target genes could be distinguished from incidental DAP-seq peak associations based on complementary data that provide functional context.…”

An introduction to a Virtual Issue on Wood Biology

“…A fast‐moving area of research seeks to use genomic and computational tools to provide integrated and comprehensive views of wood development, as well as a predictive atlas for refining breeding and selection operations. A genome‐wide assessment of open chromatin associated with active gene transcription was assayed for Eucalyptus wood‐forming tissues (Brown et al ., ). These observations were refined by the use of DAP‐seq to identify the binding sites of specific MYB transcription factors associated with wood formation.…”