Chromatin dynamics during interphase and cell division:similarities and differences between model and crop plants

Genetic information in the cell nucleus controls organismal development, responses to the environment and finally ensures own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organisation of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to the genome size, ploidy and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organisation and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits

Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing

Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates

Pathway-Based High-Throughput Chemical Screen Identifies Compounds That Decouple Heterochromatin Transformations

Heterochromatin protein 1 (HP1) facilitates the formation of repressive heterochromatin domains by recruiting histone lysine methyltransferase enzymes to chromatin, resulting in increased levels of histone H3K9me3. To identify chemical inhibitors of the HP1-heterochromatin gene repression pathway, we combined a cell-based assay that utilized chemical-mediated recruitment of HP1 to an endogenous active gene with high-throughput flow cytometry. Here we characterized small molecule inhibitors that block HP1-mediated heterochromatin formation. Our lead compounds demonstrated dose-dependent inhibition of HP1-stimulated gene repression and were validated in an orthogonal cell-based system. One lead inhibitor was improved by a change in stereochemistry, resulting in compound 2, which was further used to decouple the inverse relationship between H3K9 and H3K4 methylation states. We identified molecular components that bound compound 2, either directly or indirectly, by chemical affinity purification with a biotin-tagged derivative, followed by quantitative proteomic techniques. In summary, our pathway-based chemical screening approach resulted in the discovery of new inhibitors of HP1-mediated heterochromatin formation while identifying exciting new molecular interactions in the pathway to explore in the future. This modular platform can be expanded to test a wide range of chromatin modification pathways yielding inhibitors that are cell permeable and function in a physiologically relevant setting

A unified phylogeny-based nomenclature for histone variants

Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conventions for them has led to a variety of naming styles, multiple synonyms and misleading homographs that obscure variant relationships and complicate database searches. We propose here a unified nomenclature for variants of all five classes of histones that uses consistent but flexible naming conventions to produce names that are informative and readily searchable. The nomenclature builds on historical usage and incorporates phylogenetic relationships, which are strong predictors of structure and function. A key feature is the consistent use of punctuation to represent phylogenetic divergence, making explicit the relationships among variant subtypes that have previously been implicit or unclear. We recommend that by default new histone variants be named with organism-specific paralog-number suffixes that lack phylogenetic implication, while letter suffixes be reserved for structurally distinct clades of variants. For clarity and searchability, we encourage the use of descriptors that are separate from the phylogeny-based variant name to indicate developmental and other properties of variants that may be independent of structure

Modulational Instability of Fast Sausage Mode as One of the Possible Mechanisms for Quasiperiodic Pulsations during Solar Flares

Abstract Quasiperiodic pulsations (QPPs) are frequently observed in the entire range of the electromagnetic spectrum during solar flares, and there can be many possible mechanisms leading to this phenomenon. In the present work, we demonstrate the possibility of the generation of QPPs by a nonlinear fast sausage mode in a coronal loop. The coronal loop itself is represented by an infinitely long homogenous magnetic flux tube, which in many cases is a good approximation, and the nonlinearity of the fast sausage mode is modeled by the nonlinear Schrödinger equation (NSE) with a cubic nonlinearity. We have shown that the frequency-renormalized plane wave solution, which happens to be an exact solution of the NSE, transforms into a series of quasiperiodic oscillations (QPOs) due to the so-called modulational instability or the Benjamin–Feir instability. Our numerical solutions show that such QPOs evolve at almost every point above a certain height along the magnetic flux tube, which represents the coronal loop. As the fast sausage mode perturbs the plasma density strongly, the density perturbations caused by the QPOs of the nonlinear fast sausage mode correspondingly modulate the radiation throughout the electromagnetic spectrum, resulting in the emergence of the corresponding QPPs. This mechanism should therefore be able to describe some of the observed QPPs.</jats:p

Light behind the curtain: photoregulation of nuclear architecture and chromatin dynamics in plants

Light is a powerful stimulus regulating many aspects of plant development and phenotypic plasticity. Plants sense light through the action of specialized photoreceptor protein families that absorb different wavelengths and intensities of light. Recent discoveries in the area of photobiology have uncovered photoreversible changes in nuclear organization correlated with transcriptional regulation patterns that lead to de-etiolation and photoacclimation. Novel signalling components bridging photoreceptor activation with chromatin remodelling and regulation of gene expression have been discovered. Moreover, coregulated gene loci have been shown to relocate to the nuclear periphery in response to light. The study of photoinduced changes in nuclear architecture is a flourishing area leading to major discoveries that will allow us to better understand how highly conserved mechanisms underlying genomic reprogramming are triggered by environmental and endogenous stimuli. This review aims to discuss fundamental and innovative reports demonstrating how light triggers changes in chromatin and nuclear architecture during photomorphogenesis

A New Insight into the Linear Theory of Magnetoacoustic Waves in the Homogeneous Flux Tubes with an Abrupt Boundary

An important and interesting issue is brought to notice in the standard linear theory of the magnetoacoustic waves in the homogeneous magnetic flux tubes with an abrupt magnetic boundary, which are representative of the coronal, chromospheric, and photospheric loops of the solar atmosphere. It is shown that the dispersion relation given for the magnetoacoustic waves of such flux tubes by the linear standard theory is generally inapplicable because it does not take into account the electrodynamic boundary condition and the applicability is only restricted to the case β = 0, where β is the usual plasma parameter given by the ratio of the thermodynamic gas pressure to the magnetic pressure. This issue is then addressed, which gives us new insight into the standard linear theory of such modes, and a new dispersion relation is obtained, which is generally applicable i.e., for all β and would reduce to the earlier expression as a special case for β = 0. Finally a comparison is drawn between the dispersion curves described by the newly derived dispersion relation and its previous counterpart