Abstract: Plants as model systems have played a key role in the breakthrough discoveries of biology. The discoveries of cells (Hooke, 1665), chromosomes (von Nägeli, 1842), laws of heredity (Mendel, 1866) or mobile genetic elements (McClintock, 1950) testify to this even with just a cursory glance at history. Very dominant – and not only from a historical perspective – is the position of plant models from the point of view of epigenetics. The richness and multi-layered nature of epigenetic mechanisms in plants naturally result from their need to reprogram gene expression, not only at key moments of developmental changes, but also to adapt and respond to changes in environmental conditions. This is why plant epigenetics and the dynamics of chromatin structure are given high attention in research, and why this focus is the subject of specific conferences and workshops. Among these, the European Workshop on Plant Chromatin (EWPC) has gained its stable position since it was first organized by Claudia Koehler, Valerie Gaudin and Lars Hennig in September 2009 in Zurich. In May 2022, the 7th EWPC took place in the historical castle of Průhonice near Prague (Czech Republic), surrounded by a beautiful UNESCO-heritage botanical park. In this special issue of TPJ, we – as the organizers of the 7th EWPC – have collected review articles on topics addressed by leading research teams in the field, represented by EWPC participants who accepted our invitation to contribute to this SI. We would like to use this opportunity to thank TPJ Editor-in-Chief, Lee Sweetlove, for the support of the 7th EWPC and for the opportunity to present the discussed problems in the form of this SI. We also thank Crisanto Gutierrez, the editor of TPJ, for all his assistance and discussions concerning this SI. Craig S. Pikaard, the keynote speaker at the 7th EWPC, and his colleagues provide a perspective on past and future research on nucleolar dominance (Pikaard et al., 2023), the epigenetic phenomenon first described by McClintock almost 50 years ago (McClintock, 1934). Understanding of transcriptional regulation via nucleolar dominance recently expanded substantially, starting from its cytogenetic description, then followed by genetic and molecular details on active and repressed nucleolar organizers. The key shift in the elucidation of the mechanism came only recently with the advent of long-read single-molecule sequencing approaches. These enabled a shift from the perspective of individual copies of rRNA genes to a comprehensive view of the entire rDNA loci. Naturally, emerging questions and even deeper digging, for example, into nucleolar dominance initiation, arise with this current knowledge, which will require further research effort. Although, as the authors conclude, 'the allure of science lies in the satisfaction of knowing that our reach can exceed our grasp'. The review by Ioanna Kakoulidou and Frank Johannes focuses on the dynamics of cytosine DNA methylation in plant hybrids (Kakoulidou & Johannes, 2023). DNA methylation is a prominent modification that is predominantly used by plants to suppress the activity of genomic parasites but which is also important for the regulation of gene transcription. Upon hybridization, the DNA methylation machinery must distribute modifications and organize chromatin in a way that reaches a new equilibrium. However, assessing these changes in the genomic regions lacking genetic polymorphisms is challenging. The authors propose models and suggest how to address this issue using genomic tools. Lauriane Simon and Aline V. Probst offer a comprehensive view of epigenetic chromatin changes. They discuss the consequences of these changes for reprogramming gene activity and the 3D chromatin structure in the nucleus, from the nucleosomal level to chromosomal territories (Simon & Probst, 2024). They also address important and still partially enigmatic issues of the maintenance of chromatin states through DNA replication and reprogramming of the epigenome in certain developmental phase transitions. They also highlight the importance of scaling down RNA-Seq, ChIP-Seq and Hi-C analyses to a few specific cells or even to the single-cell level to dissect mechanisms of epigenome reprogramming in key moments of plant development. Anis Meschini and Stafanie Rosa focus their review on a related topic of chromatin mobility in plant cells (Meschichi & Rosa, 2024). In particular, they describe changes in chromatin (and chromosome) localisation during the cell cycle and in cell differentiation. They further address the topic of increased chromatin mobility induced by DNA damage. Intrinsic factors affecting chromatin mobility are also discussed, such as chromosome or nuclear localization, ATP-dependent remodelling complexes and links between chromatin and the cytoskeleton, for example, through the LINC (linker of the nucleoskeleton to the cytoskeleton) complex. The review of Marie-Edith Chaboute and Alexander Berr's lab (Dupouy et al., 2024) describes how the components of the nuclear envelope sense outside signals and transmit them to the interior of the plant nucleus. An example of this is the sensing of mechanical force, which causes cell wall deformation in plants, being transmitted via microtubules and microfilaments to the nuclear envelope. They compare protein complexes known in mammals and compare them to the plant system – for example, the LINC complex connecting the nuclear envelope to nucleoskeleton lamins in mammals, which links to heterochromatin and helps to maintain cellular shape. The CROWDED NUCLEI proteins mediate lamin functions in plants, directly interacting with LINC components and a number of chromatin factors. The authors point to the existence of a tight connection between the nuclear envelope, nucleoskeleton and chromatin organization. They also discuss some known examples of chromocenter re-organization upon stretching or hyperosmotic stress in plants as well as the behaviour of euchromatic sites, and the role of the nuclear envelope during development, cell cycle and DNA damage. Amanda S. Camara, Ivona Kubalova and Veit Schubert bring a comprehensive overview of chromatin organization, focusing on how coiled chromatin thread, called chromonema, assembles into chromatids during mitosis (Câmara et al., 2023). Starting with the lower-order structure, they stress that a 30-nm fibre is unlikely to form a structural unit, as revealed by electron microscopy. The authors then focus on the higher-order structure and point to the non-helical model, based on the condensed network of chromatin and linker proteins. Methods with great potential for the investigation of non-histone proteins (e.g., SMC complex) to chromatin coiling are presented in chronological order, including the most advanced approaches, such as Hi-C, oligo FISH or polymer simulation. Kerckhofs and Schubert (2023) review epigenetic mechanisms that are conserved in Archaeplastida, the primary endosymbiotic lineages comprising mainly red algae, green algae and land plants. They also discuss the contribution of nuclear envelope proteins in chromatin distribution and stress responses. They focus on a major developmental epigenetic regulator, polycomb repressive complex 2 (PRC2), and highlight the conservation and evolution of its function. The authors argue for a conserved function of PRC2 in major life phase transitions between the gametophyte and the sporophyte, and in gene and genome dosage compensation. In contrast, they highlight the evolutionary differences in the genome-wide targeting of H3K27me3, the catalytic product of PRC2, proposing a shift in H3K27me3 distribution from repetitive sequences to protein-coding genes in the course of evolution. A contribution from Klaus D. Grasser's group (Obermeyer et al., 2023) provides an interesting overview of an important regulatory level in gene expression on nucleosomal templates – transcript elongation by RNA polymerase II (RNAPII). This regulation is mediated through transcript elongation factors (TEFs) and histone chaperones. Interestingly, despite similarities in the structure of nucleosomes, RNAPII and TEFs, there are differences at this level of transcriptional regulation between Arabidopsis, and humans or yeast. For example, while human and yeast RNAPII show frequent pausing near the transcriptional start site (TSS), this pausing is not apparent in Arabidopsis, which is reflected in the lack of accumulation of S5 phosphorylation in the C-terminal domain of RNAPII, typical for human and yeast RNAPII near the TSS. Lermontova and colleagues (2023) bring an updated understanding of centromere organization and propose mechanisms of sequence-independent centromere formation. Despite the conserved function of centromeres and the kinetochore, the centromeric sequence and the composition of kinetochore complexes differ. Loading of CENH3, a conserved marker for the centromere, may contribute to centromere establishment but the mechanisms of its targeting are far from understood. The authors highlight interactions of CENH3 loading and kinetochore assembly factors with centromeric DNA and non-coding transcripts originating from centromeres, proposing their role in centromere and perhaps even neocentromere formation. We do believe these examples of currently developing knowledge in the field of plant chromatin structure and epigenetics, reflecting the 7th EWPC content, will be of interest to the broad readership of the Plant Journal.