Phase separation of chromatin and small RNA pathways in plants

Gene expression can be modulated by epigenetic mechanisms, including chromatin modifications and small regulatory RNAs. These pathways are unevenly distributed within a cell and usually take place in specific intracellular regions. Unfortunately, the fundamental driving force and biological relevance of such spatial differentiation is largely unknown. Liquid–liquid phase separation (LLPS) is a natural propensity of demixing liquid phases and has been recently suggested to mediate the formation of biomolecular condensates that are relevant to diverse cellular processes. LLPS provides a mechanistic explanation for the self-assembly of subcellular structures by which the efficiency and specificity of certain cellular reactions are achieved. In plants, LLPS has been observed for several key factors in the chromatin and small RNA pathways. For example, the formation of facultative and obligate heterochromatin involves the LLPS of multiple relevant factors. In addition, phase separation is observed in a set of proteins acting in microRNA biogenesis and the small interfering RNA pathway. In this Focused Review, we highlight and discuss the recent findings regarding phase separation in the epigenetic mechanisms of plants.     

Common ground: small RNA programming and chromatin modifications

Epigenetic mechanisms regulate genome structure and expression profiles in eukaryotes. RNA interference (RNAi) and other small RNA-based chromatin-modifying activities can act to reset the epigenetic landscape at defined chromatin domains. Centromeric heterochromatin assembly is a RNAi-dependent process in the fission yeast Schizosaccharomyces pombe, and provides a paradigm for detailed examination of such epigenetic processes. Here we review recent progress in understanding the mechanisms that underpin RNAi-mediated heterochromatin formation in S. pombe. We discuss recent analyses of the events that trigger RNAi and manipulations which uncouple RNAi and chromatin modification. Finally we provide an overview of similar molecular machineries across species where related small RNA pathways appear to drive the epigenetic reprogramming in germ cells and/or during early development in metazoans.     

Functions of DNA methyltransferase 3‐like in germ cells and beyond

DNA methyltransferase 3‐like (DNMT3L) is one of the key players in de novo DNA methylation of imprinting control elements and retrotransposons, which occurs after genome‐wide epigenetic erasure during germ cell development. In this review, we summarise the biochemical properties of DNMT3L and discuss the possible mechanisms behind DNMT3L‐mediated imprinting establishment and retrotransposon silencing in germ cells. We also discuss possible connections between DNMT3L and non‐coding RNA‐mediated epigenetic remodelling, the roles of DNMT3L in germ cell development and the implications in stem cell and cancer research.     

配子体自交不亲和信号转导的研究进展

自然界中大多数自交不亲和（self-incompatibility, SI）显花植物表现为配子体SI。配子体SI植物虽然都具有其SI的功能而阻止自我受精,但它们采取的信号转导途径是不同的。目前关于配子体SI信号转导的途径主要有两种：一是茄科、玄参科、蔷薇科中以雌蕊S-RNase为基础的信号转导途径;另一是罂粟科中以花粉管胞质自由钙离子为第二信使的转导途径。文章就配子体SI信号转导的研究进展作一综述。     

Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis

Trimethylation of histone H3 lysine 27 (H3K27me3) plays critical roles in regulating animal development, and in several cases, H3K27me3 is also required for the proper expression of developmentally important genes in plants. However, the extent to which H3K27me3 regulates plant genes on a genome-wide scale remains unknown. In addition, it is not clear whether the establishment and spreading of H3K27me3 occur through the same mechanisms in plants and animals. We identified regions containing H3K27me3 in the genome of the flowering plant Arabidopsis thaliana using a high-density whole-genome tiling microarray. The results suggest that H3K27me3 is a major silencing mechanism in plants that regulates an unexpectedly large number of genes in Arabidopsis (~4,400), and that the maintenance of H3K27me3 is largely independent of other epigenetic pathways, such as DNA methylation or RNA interference. Unlike in animals, where H3K27m3 occupies large genomic regions, in Arabidopsis, we found that H3K27m3 domains were largely restricted to the transcribed regions of single genes. Furthermore, unlike in animals systems, H3K27m3 domains were not preferentially associated with low–nucleosome density regions. The results suggest that different mechanisms may underlie the establishment and spreading of H3K27me3 in plants and animals.     

Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis

Trimethylation of histone H3 lysine 27 (H3K27me3) plays critical roles in regulating animal development, and in several cases, H3K27me3 is also required for the proper expression of developmentally important genes in plants. However, the extent to which H3K27me3 regulates plant genes on a genome-wide scale remains unknown. In addition, it is not clear whether the establishment and spreading of H3K27me3 occur through the same mechanisms in plants and animals. We identified regions containing H3K27me3 in the genome of the flowering plant Arabidopsis thaliana using a high-density whole-genome tiling microarray. The results suggest that H3K27me3 is a major silencing mechanism in plants that regulates an unexpectedly large number of genes in Arabidopsis (~4,400), and that the maintenance of H3K27me3 is largely independent of other epigenetic pathways, such as DNA methylation or RNA interference. Unlike in animals, where H3K27m3 occupies large genomic regions, in Arabidopsis, we found that H3K27m3 domains were largely restricted to the transcribed regions of single genes. Furthermore, unlike in animals systems, H3K27m3 domains were not preferentially associated with low–nucleosome density regions. The results suggest that different mechanisms may underlie the establishment and spreading of H3K27me3 in plants and animals.     

Genesis of cells of apical meristems and realization of gametophytic apomixis in flowering plants

Based on our own and literature data on peculiarities of caryotypical variability, we concluded that gametophytic apomixis is naturally accompanied with phenomena of poly-, aneu-, and mixoploidy and that apomicts have genome instability manifesting at the level of meristematic somatic cells. In this connection, a hypothesis is substantiated that realization of this mode of seed reproduction in flowering plants is caused by modification of systems of cell cycle control, following after acts of hybridogenesis and/or polyploidization. It is concluded that instability of the seed reproduction system by gametophytic apomixis manifests not only at the stage of choice of a seed reproduction pathway (apomeiosis-euspory; apozygosis-zygosis) but also in all the cycles of reproduction of the cells of a germ line in plant ontogenesis.     

Genesis of cells of apical meristems and realization of gametophytic apomixis in flowering plants

Based on our own and literature data on peculiarities of caryotypical variability, we concluded that gametophytic apomixis is naturally accompanied with phenomena of poly-, aneu-, and mixoploidy and that apomicts have genome instability manifesting at the level of meristematic somatic cells. In this connection, a hypothesis is substantiated that realization of this mode of seed reproduction in flowering plants is caused by modification of systems of cell cycle control, following after acts of hybridogenesis and/or polyploidization. It is concluded that instability of the seed reproduction system by gametophytic apomixis manifests not only at the stage of choice of a seed reproduction pathway (apomeiosis—euspory; apozygosis—zygosis) but also in all the cycles of reproduction of the cells of a germ line in plant ontogenesis.