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Identification and functional evaluation of accessible chromatin associated with wood formation in Eucalyptus grandis
Author(s) -
Brown Katrien,
Takawira Lazarus T.,
O'Neill Marja M.,
Mizrachi Eshchar,
Myburg Alexander A.,
Hussey Steven G.
Publication year - 2019
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.15897
Subject(s) - biology , chromatin , myb , transcription factor , genetics , epigenetics , gene , dna , context (archaeology) , computational biology , paleontology
Summary 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 DN ase I Hypersensitive Sites ( DHS s) 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 (Egr MYB ) transcription factors using DAP ‐seq, reconstructed protein‐ DNA networks of predicted targets based on binding sites within or outside DHS s and assessed biological enrichment of these networks with published datasets. 25 319 identified immature xylem DHS s 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 Egr MYB 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 DHS s in E. grandis immature xylem, most of which are intergenic, are of functional significance to gene regulation in this tissue.