Abstract
Chromatin is a major determinant in the regulation of virtually all DNA-dependent processes. Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. The evolutionarily conserved DEK domain-containing protein is implicated in important chromatin-related processes in animals, but little is known about its DNA targets and protein interaction partners. In plants, the role of DEK has remained elusive. In this work, we identified DEK3 as a chromatin-associated protein in Arabidopsis thaliana. DEK3 specifically binds histones H3 and H4. Purification of other proteins associated with nuclear DEK3 also established DNA topoisomerase 1α and proteins of the cohesion complex as in vivo interaction partners. Genome-wide mapping of DEK3 binding sites by chromatin immunoprecipitation followed by deep sequencing revealed enrichment of DEK3 at protein-coding genes throughout the genome. Using DEK3 knockout and overexpressor lines, we show that DEK3 affects nucleosome occupancy and chromatin accessibility and modulates the expression of DEK3 target genes. Furthermore, functional levels of DEK3 are crucial for stress tolerance. Overall, data indicate that DEK3 contributes to modulation of Arabidopsis chromatin structure and function.
Highlights
In the nucleus of eukaryotes, DNA is tightly packed into chromatin
We provide evidence that DEK3 is a plant chromatin protein involved in regulating nucleosome occupancy and gene expression
DEK3 was immunoprecipitated with green fluorescent protein (GFP) antibodies from nuclear extracts of seedlings expressing DEK3CFP
Summary
The chromatin structure has profound implications on gene expression, DNA replication, and repair, and it plays an important role in diverse processes, including development and responses to environmental changes (Ho and Crabtree, 2010; Li and Reinberg, 2011; van Zanten et al, 2012; Gentry and Hennig, 2014; Han and Wagner, 2014). Genomic DNA is wrapped around histone octamers to form nucleosomes, the primary level of chromatin organization. A multitude of diverse proteins such as histone chaperones, histone-modifying enzymes, ATPdependent chromatin remodeling complexes, and nonhistone architectural proteins alter local chromatin properties and/or affect higher order chromatin structure (Ho and Crabtree, 2010; Luger et al, 2012; Gentry and Hennig, 2014)
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