Arabidopsis Chromatin Assembly Factor 1 is required for occupancy and position of a subset of nucleosomes

• Published in: The Plant journal : for cell and molecular biology Vol. 92; no. 3; pp. 363 - 374
• Main Authors: Muñoz‐Viana, Rafael, Wildhaber, Thomas, Trejo‐Arellano, Minerva S., Mozgová, Iva, Hennig, Lars
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.11.2017
• Subjects: Arabidopsis; Arabidopsis - genetics; Arabidopsis - immunology; Arabidopsis - metabolism; Arabidopsis thaliana; Botanik; Botany; CAF‐1; Chromatin; Chromatin - genetics; Chromatin Assembly and Disassembly - genetics; Chromatin Assembly Factor-1 - genetics; Chromatin Assembly Factor-1 - metabolism; Chromatin remodeling; Deoxyribonucleic acid; DNA; DNA biosynthesis; DNA repair; DNA Repair - genetics; DNA Replication - genetics; Fitness; Gene expression; Genes; Genomes; GSE87421; Mutation; Nucleosomes; Nucleosomes - genetics; Nucleosomes - metabolism; plant defense; Plant Immunity - genetics; Plant resistance; Promoter Regions, Genetic - genetics; Sequence Analysis, DNA; Transcription; Transcription Initiation Site; Arabidopsis thaliana; CAF-1; plant defense; chromatin; GSE87421
• ISSN: 0960-7412; 1365-313X; 1365-313X
• DOI: 10.1111/tpj.13658

Summary Chromatin Assembly Factor 1 (CAF‐1) is a major nucleosome assembly complex which functions particularly during DNA replication and repair. Here we studied how the nucleosome landscape changes in a CAF‐1 mutant in the model plant Arabidopsis thaliana. Globally, most nucleosomes were not affected by loss of CAF‐1, indicating the presence of efficient alternative nucleosome assemblers. Nucleosomes that we found depleted in the CAF‐1 mutant were enriched in non‐transcribed regions, consistent with the notion that CAF‐1‐independent nucleosome assembly can compensate for loss of CAF‐1 mainly in transcribed regions. Depleted nucleosomes were particularly enriched in proximal promoters, suggesting that CAF‐1‐independent nucleosome assembly mechanisms are often not efficient upstream of transcription start sites. Genes related to plant defense were particularly prone to lose nucleosomes in their promoters upon CAF‐1 depletion. Reduced nucleosome occupancy at promoters of many defense‐related genes is associated with a primed gene expression state that may considerably increase plant fitness by facilitating plant defense. Together, our results establish that the nucleosome landscape in Arabidopsis is surprisingly robust even in the absence of the dedicated nucleosome assembly machinery CAF‐1 and that CAF‐1‐independent nucleosome assembly mechanisms are less efficient in particular genome regions. Significance Statement Lack of chromatin assembly factor 1 can be globally compensated for but compensation is less efficient in promoters of many defense‐related genes confirming a connection between nucleosome occupancy and gene expression states primed for defense.