Mind the gap: Epigenetic regulation of chromatin accessibility in plants

Abstract

Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central in regulating these processes, determining chromatin accessibility by limiting access to DNA for various proteins, and acting as important signaling hubs. The association of nucleosomes to DNA and the folding of chromatin into higher-order structures are strongly influenced by a variety of epigenetic marks, including DNA methylation, histone variants, and histone post-translational modifications. Additionally, a wide array of chaperones and ATP-dependent remodelers regulate various aspects of nucleosome biology, including assembly, deposition, and positioning. This review provides an overview of recent advances in our mechanistic understanding of how nucleosomes and chromatin organization are regulated by epigenetic marks and remodelers in plants. Furthermore, we present current technologies for profiling chromatin accessibility and organization.

Paulownia Witches’ Broom Disease: A Comprehensive Review

“…Histone methylation and acetylation can influence genome accessibility, at levels ranging from local nucleosome dynamics to the folding of higher chromatin structure. Both methylation and acetylation promote open chromatin conformation and positively influence the genome accessibility [95]. Chromatin immunoprecipitation sequencing (ChIPseq) was used to profile three histone marks, the methylation of histone H3 at lysine 4 (H3K4me3), the methylation of histone H3 at lysine 36 (H3K36me3) and the acetylation of histone H3 at lysine 9 (H3K9ac), among healthy, diseased and MMS-treated diseased P. fortunei plantlets grown in vitro [74,75].…”

“…DNA methylation participates in various nuclear processes such as gene expression, DNA repair and recombination. Various studies have indicated that DNA methylation at gene boundaries contributes to a differential gene expression in response to pathogens [95]. Methylation-sensitive amplification polymorphism (MSAP) analysis revealed that the DNA methylation level of healthy plantlets is higher than the PaWB-diseased ones.…”

Vegetal memory through the lens of transcriptomic changes – recent progress and future practical prospects for exploiting plant transcriptional memory

“…The existing epigenetic patterns with distinct distribution and level of methylation, acetylation and other epigenetic marks can form epialleles, which are stably carried on to the future generations. 46 …”

The structure of the R2T complex reveals a different architecture of the related HSP90 co-chaperones R2T and R2TP

“…Both proteins have an ATPase domain which is inserted by the prominent Domain II (DII) with a characteristic oligonucleotide/oligosaccharide binding-fold (OB-fold) responsible for protein-protein interactions. Rvb1/RuvBL1 and Rvb2/RuvBL2 are shared with other complexes involved in chromatin remodeling, such as SWR1 and INO80-C (Candela-Ferré et al, 2024). Yeast Tah1 is a small protein (12 KDa) consisting almost exclusively of a carboxylate clamp-type TPR domain that interacts with the C-terminal peptide MEEVD of HSP90 and is thus responsible for the recruitment of the chaperone to the R2TP complex (Zhao et al, 2005).…”