Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance

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

Plant memory plays an important role in the efficient and rapid acclimation to a swiftly changing environment. In addition, since plant memory can be inherited, it is also of adaptive and evolutionary importance. The ability of a plant to store, retain, retrieve and delete information on acquired experience is based on cellular, biochemical and molecular networks in the plants. This review offers an up-to-date overview on the formation, types, checkpoints of plant memory based on our current knowledge and focusing on its transcriptional aspects, the transcriptional memory. Roles of long and small non-coding RNAs are summarized in the regulation, formation and the cooperation between the different layers of the plant memory, i.e. in the establishment of epigenetic changes associated with memory formation in plants. The RNA interference mechanisms at the RNA and DNA level and the interplays between them are also presented. Furthermore, this review gives an insight of how exploitation of plant transcriptional memory may provide new opportunities for elaborating promising cost-efficient, and effective strategies to cope with the ever-changing environmental perturbations, caused by climate change. The potentials of plant memory-based methods, such as crop priming, cross acclimatization, memory modification by miRNAs and associative use of plant memory, in the future's agriculture are also discussed.

Dissecting Mechanisms of Epigenetic Memory Through Computational Modeling

Understanding the mechanistic basis of epigenetic memory has proven to be a difficult task due to the underlying complexity of the systems involved in its establishment and maintenance. Here, we review the role of computational modeling in helping to unlock this complexity, allowing the dissection of intricate feedback dynamics. We focus on three forms of epigenetic memory encoded in gene regulatory networks, DNA methylation, and histone modifications and discuss the important advantages offered by plant systems in their dissection. We summarize the main modeling approaches involved and highlight the principal conceptual advances that the modeling has enabled through iterative cycles of predictive modeling and experiments. Lastly, we discuss remaining gaps in our understanding and how intertwined theory and experimental approaches might help in their resolution.

A CPF-like phosphatase module links transcription termination to chromatin silencing

The interconnections between co-transcriptional regulation, chromatin environment, and transcriptional output remain poorly understood. Here, we investigate the mechanism underlying RNA 3' processing-mediated Polycomb silencing of Arabidopsis FLOWERING LOCUS C (FLC). We show a requirement for ANTHESIS PROMOTING FACTOR 1 (APRF1), a homolog of yeast Swd2 and human WDR82, known to regulate RNA polymerase II (RNA Pol II) during transcription termination. APRF1 interacts with TYPE ONE SERINE/THREONINE PROTEIN PHOSPHATASE 4 (TOPP4) (yeast Glc7/human PP1) and LUMINIDEPENDENS (LD), the latter showing structural features found in Ref2/PNUTS, all components of the yeast and human phosphatase module of the CPF 3' end-processing machinery. LD has been shown to co-associate in vivo with the histone H3 K4 demethylase FLOWERING LOCUS D (FLD). This work shows how the APRF1/LD-mediated polyadenylation/termination process influences subsequent rounds of transcription by changing the local chromatin environment at FLC.

Proximal termination generates a transcriptional state that determines the rate of establishment of Polycomb silencing

The mechanisms and timescales controlling de novo establishment of chromatin-mediated transcriptional silencing by Polycomb repressive complex 2 (PRC2) are unclear. Here, we investigate PRC2 silencing at Arabidopsis FLOWERING LOCUS C (FLC), known to involve co-transcriptional RNA processing, histone demethylation activity, and PRC2 function, but so far not mechanistically connected. We develop and test a computational model describing proximal polyadenylation/termination mediated by the RNA-binding protein FCA that induces H3K4me1 removal by the histone demethylase FLD. H3K4me1 removal feeds back to reduce RNA polymerase II (RNA Pol II) processivity and thus enhance early termination, thereby repressing productive transcription. The model predicts that this transcription-coupled repression controls the level of transcriptional antagonism to PRC2 action. Thus, the effectiveness of this repression dictates the timescale for establishment of PRC2/H3K27me3 silencing. We experimentally validate these mechanistic model predictions, revealing that co-transcriptional processing sets the level of productive transcription at the locus, which then determines the rate of the ON-to-OFF switch to PRC2 silencing.

COOLAIR and PRC2 function in parallel to silence FLC during vernalization

Noncoding transcription induces chromatin changes that can mediate environmental responsiveness, but the causes and consequences of these mechanisms are still unclear. Here, we investigate how antisense transcription (termed COOLAIR) interfaces with Polycomb Repressive Complex 2 (PRC2) silencing during winter-induced epigenetic regulation of Arabidopsis FLOWERING LOCUS C (FLC). We use genetic and chromatin analyses on lines ineffective or hyperactive for the antisense pathway in combination with computational modeling to define the mechanisms underlying FLC repression. Our results show that FLC is silenced through pathways that function with different dynamics: a COOLAIR transcription-mediated pathway capable of fast response and in parallel a slow PRC2 switching mechanism that maintains each allele in an epigenetically silenced state. Components of both the COOLAIR and PRC2 pathways are regulated by a common transcriptional regulator (NTL8), which accumulates by reduced dilution due to slow growth at low temperature. The parallel activities of the regulatory steps, and their control by temperature-dependent growth dynamics, create a flexible system for registering widely fluctuating natural temperature conditions that change year on year, and yet ensure robust epigenetic silencing of FLC.

Design principles of 3D epigenetic memory systems

Cells remember their identities, in part, by using epigenetic marks-chemical modifications placed along the genome. How can mark patterns remain stable over cell generations despite their constant erosion by replication and other processes? We developed a theoretical model that reveals that three-dimensional (3D) genome organization can stabilize epigenetic memory as long as (i) there is a large density difference between chromatin compartments, (ii) modifying "reader-writer" enzymes spread marks in three dimensions, and (iii) the enzymes are limited in abundance relative to their histone substrates. Analogous to an associative memory that encodes memory in neuronal connectivity, mark patterns are encoded in a 3D network of chromosomal contacts. Our model provides a unified account of diverse observations and reveals a key role of 3D genome organization in epigenetic memory.

Is winter coming? Impact of the changing climate on plant responses to cold temperature

Climate change is causing alterations in annual temperature regimes worldwide. Important aspects of this include the reduction of winter chilling temperatures as well as the occurrence of unpredicted frosts, both significantly affecting plant growth and yields. Recent studies advanced the knowledge of the mechanisms underlying cold responses and tolerance in the model plant Arabidopsis thaliana. However, how these cold-responsive pathways will readjust to ongoing seasonal temperature variation caused by global warming remains an open question. In this review, we highlight the plant developmental programmes that depend on cold temperature. We focus on the molecular mechanisms that plants have evolved to adjust their development and stress responses upon exposure to cold. Covering both genetic and epigenetic aspects, we present the latest insights into how alternative splicing, noncoding RNAs and the formation of biomolecular condensates play key roles in the regulation of cold responses. We conclude by commenting on attractive targets to accelerate the breeding of increased cold tolerance, bringing up biotechnological tools that might assist in overcoming current limitations. Our aim is to guide the reflection on the current agricultural challenges imposed by a changing climate and to provide useful information for improving plant resilience to unpredictable cold regimes.

Evolutionary Dynamics of FLC-like MADS-Box Genes in Brassicaceae

MADS-box genes encode transcription factors that play important roles in the development and evolution of plants. There are more than a dozen clades of MADS-box genes in angiosperms, of which those with functions in the specification of floral organ identity are especially well-known. From what has been elucidated in the model plant Arabidopsis thaliana, the clade of FLC-like MADS-box genes, comprising FLC-like genes sensu strictu and MAF-like genes, are somewhat special among the MADS-box genes of plants since FLC-like genes, especially MAF-like genes, show unusual evolutionary dynamics, in that they generate clusters of tandemly duplicated genes. Here, we make use of the latest genomic data of Brassicaceae to study this remarkable feature of the FLC-like genes in a phylogenetic context. We have identified all FLC-like genes in the genomes of 29 species of Brassicaceae and reconstructed the phylogeny of these genes employing a Maximum Likelihood method. In addition, we conducted selection analyses using PAML. Our results reveal that there are three major clades of FLC-like genes in Brassicaceae that all evolve under purifying selection but with remarkably different strengths. We confirm that the tandem arrangement of MAF-like genes in the genomes of Brassicaceae resulted in a high rate of duplications and losses. Interestingly, MAF-like genes also seem to be prone to transposition. Considering the role of FLC-like genes sensu lato (s.l.) in the timing of floral transition, we hypothesize that this rapid evolution of the MAF-like genes was a main contributor to the successful adaptation of Brassicaceae to different environments.

Integrating analog and digital modes of gene expression at Arabidopsis FLC

Quantitative gene regulation at the cell population level can be achieved by two fundamentally different modes of regulation at individual gene copies. A 'digital' mode involves binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state, while an 'analog' mode involves graded expression levels at each gene copy. At the Arabidopsis floral repressor FLOWERING LOCUS C (FLC), 'digital' Polycomb silencing is known to facilitate quantitative epigenetic memory in response to cold. However, whether FLC regulation before cold involves analog or digital modes is unknown. Using quantitative fluorescent imaging of FLC mRNA and protein, together with mathematical modeling, we find that FLC expression before cold is regulated by both analog and digital modes. We observe a temporal separation between the two modes, with analog preceding digital. The analog mode can maintain intermediate expression levels at individual FLC gene copies, before subsequent digital silencing, consistent with the copies switching OFF stochastically and heritably without cold. This switch leads to a slow reduction in FLC expression at the cell population level. These data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways can be integrated.

Epigenetic switching with asymmetric bridging interactions

Gene expression states are often stably sustained in cis despite massively disruptive events like DNA replication. This is achieved by on-going enzymatic activity that maintains parts of the DNA in either heterochromatic (packed) or euchromatic (free) states, each of which is stabilized by both positive feedback and bridging interactions between individual nucleosomes. In contrast to condensed matter, however, the dynamics is not only governed by equilibrium binding interactions but is also mediated by enzymes that recognize and act on specific amino acid tails of the nucleosomes. The mechanical result is that some nucleosomes can bind to one another and form tightly packed polymer configurations, whereas others remain unbound and form free, noncompact polymer configurations. Here, we study the consequences of such an asymmetric interaction pattern on the dynamics of epigenetic switching. We develop a 3D polymer model and show that traits associated with epigenetic switching, such as bistability and epigenetic memory, are permitted by such a model. We find, however, that the experimentally observed burst-like nature of some epigenetic switches is difficult to reproduce by this biologically motivated interaction. Instead, the behavior seen in experiments can be explained by introducing partial confinement, which particularly affects the euchromatic regions of the chromosome.

The molecular basis of heterochromatin assembly and epigenetic inheritance

Heterochromatin plays a fundamental role in gene regulation, genome integrity, and silencing of repetitive DNA elements. Histone modifications are essential for the establishment of heterochromatin domains, which is initiated by the recruitment of histone-modifying enzymes to nucleation sites. This leads to the deposition of histone H3 lysine-9 methylation (H3K9me), which provides the foundation for building high-concentration territories of heterochromatin proteins and the spread of heterochromatin across extended domains. Moreover, heterochromatin can be epigenetically inherited during cell division in a self-templating manner. This involves a "read-write" mechanism where pre-existing modified histones, such as tri-methylated H3K9 (H3K9me3), support chromatin association of the histone methyltransferase to promote further deposition of H3K9me. Recent studies suggest that a critical density of H3K9me3 and its associated factors is necessary for the propagation of heterochromatin domains across multiple generations. In this review, I discuss the key experiments that have highlighted the importance of modified histones for epigenetic inheritance.

Head-to-tail polymerization by VEL proteins underpins cold-induced Polycomb silencing in flowering control

Transcriptional silencing through the Polycomb silencing machinery utilizes a "read-write" mechanism involving histone tail modifications. However, nucleation of silencing and long-term stable transmission of the silenced state also requires P-olycomb Repressive Complex 2 (PRC2) accessory proteins, whose molecular role is poorly understood. The Arabidopsis VEL proteins are accessory proteins that interact with PRC2 to nucleate and propagate silencing at the FLOWERING LOCUS C (FLC) locus, enabling early flowering in spring. Here, we report that VEL proteins contain a domain related to an atypical four-helix bundle that engages in spontaneous concentration-dependent head-to-tail polymerization to assemble dynamic biomolecular condensates. Mutations blocking polymerization of this VEL domain prevent Polycomb silencing at FLC. Plant VEL proteins thus facilitate assembly of dynamic multivalent Polycomb complexes required for inheritance of the silenced state.

VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC

Polycomb (PcG) silencing is crucial for development, but how targets are specified remains incompletely understood. The cold-induced Polycomb Repressive Complex 2 (PRC2) silencing of Arabidopsis thaliana FLOWERING LOCUS C (FLC) provides an excellent system to elucidate PcG regulation. Association of the DNA binding protein VAL1 to FLC PcG nucleation regionis an important step. VAL1 co-immunoprecipitates APOPTOSIS AND SPLICING ASSOCIATED PROTEIN (ASAP) complex and PRC1. Here, we show that ASAP and PRC1 are necessary for co-transcriptional repression and chromatin regulation at FLC. ASAP mutants affect FLC transcription in warm conditions, but the rate of FLC silencing in the cold is unaffected. PRC1-mediated H2Aub accumulation increases at the FLC nucleation region during cold, but unlike the PRC2-delivered H3K27me3, does not spread across the locus. H2Aub thus involved in the transition to epigenetic silencing at FLC, facilitating H3K27me3 accumulation and long-term epigenetic memory. Overall, our work highlights the importance of VAL1 as an assembly platform co-ordinating activities necessary for epigenetic silencing at FLC.

Distinct silencer states generate epigenetic states of heterochromatin

Heterochromatic loci can exhibit different transcriptional states in genetically identical cells. A popular model posits that the inheritance of modified histones is sufficient for inheritance of the silenced state. However, silencing inheritance requires silencers and therefore cannot be driven by the inheritance of modified histones alone. To address these observations, we determined the chromatin architectures produced by strong and weak silencers in Saccharomyces. Strong silencers recruited Sir proteins and silenced the locus in all cells. Strikingly, weakening these silencers reduced Sir protein recruitment and stably silenced the locus in some cells; however, this silenced state could probabilistically convert to an expressed state that lacked Sir protein recruitment. Additionally, changes in the constellation of silencer-bound proteins or the concentration of a structural Sir protein modulated the probability that a locus exhibited the silenced or expressed state. These findings argued that distinct silencer states generate epigenetic states and regulate their dynamics.

Understanding plant stress memory response for abiotic stress resilience: Molecular insights and prospects

As sessile species and without the possibility of escape, plants constantly face numerous environmental stresses. To adapt in the external environmental cues, plants adjust themselves against such stresses by regulating their physiological, metabolic and developmental responses to external environmental cues. Certain environmental stresses rarely occur during plant life, while others, such as heat, drought, salinity, and cold are repetitive. Abiotic stresses are among the foremost environmental variables that have hindered agricultural production globally. Through distinct mechanisms, these stresses induce various morphological, biochemical, physiological, and metabolic changes in plants, directly impacting their growth, development, and productivity. Subsequently, plant's physiological, metabolic, and genetic adjustments to the stress occurrence provide necessary competencies to adapt, survive and nurture a condition known as "memory." This review emphasizes the advancements in various epigenetic-related chromatin modifications, DNA methylation, histone modifications, chromatin remodeling, phytohormones, and microRNAs associated with abiotic stress memory. Plants have the ability to respond quickly to stressful situations and can also improve their defense systems by retaining and sustaining stressful memories, allowing for stronger or faster responses to repeated stressful situations. Although there are relatively few examples of such memories, and no clear understanding of their duration, taking into consideration plenty of stresses in nature. Understanding these mechanisms in depth could aid in the development of genetic tools to improve breeding techniques, resulting in higher agricultural yield and quality under changing environmental conditions.

A cis-acting mechanism mediates transcriptional memory at Polycomb target genes in mammals

Epigenetic inheritance of gene expression states enables a single genome to maintain distinct cellular identities. How histone modifications contribute to this process remains unclear. Using global chromatin perturbations and local, time-controlled modulation of transcription, we establish the existence of epigenetic memory of transcriptional activation for genes that can be silenced by the Polycomb group. This property emerges during cell differentiation and allows genes to be stably switched after a transient transcriptional stimulus. This transcriptional memory state at Polycomb targets operates in cis; however, rather than relying solely on read-and-write propagation of histone modifications, the memory is also linked to the strength of activating inputs opposing Polycomb proteins, and therefore varies with the cellular context. Our data and computational simulations suggest a model whereby transcriptional memory arises from double-negative feedback between Polycomb-mediated silencing and active transcription. Transcriptional memory at Polycomb targets thus depends not only on histone modifications but also on the gene-regulatory network and underlying identity of a cell.

Cell division in the shoot apical meristem is a trigger for miR156 decline and vegetative phase transition in Arabidopsis

What determines the rate at which a multicellular organism matures is a fundamental question in biology. In plants, the decline of miR156 with age serves as an intrinsic, evolutionarily conserved timer for the juvenile-to-adult phase transition. However, the way in which age regulates miR156 abundance is poorly understood. Here, we show that the rate of decline in miR156 is correlated with developmental age rather than chronological age. Mechanistically, we found that cell division in the apical meristem is a trigger for miR156 decline. The transcriptional activity of MIR156 genes is gradually attenuated by the deposition of the repressive histone mark H3K27me3 along with cell division. Our findings thus provide a plausible explanation of why the maturation program of a multicellular organism is unidirectional and irreversible under normal growth conditions and suggest that cell quiescence is the fountain of youth in plants.

Transcriptional memory and response to adverse temperatures in plants

Temperature is one of the major environmental signals controlling plant development, geographical distribution, and seasonal behavior. Plants perceive adverse temperatures, such as high, low, and freezing temperatures, as stressful signals that can cause physiological defects and even death. As sessile organisms, plants have evolved sophisticated mechanisms to adapt to recurring stressful environments through changing gene expression or transcriptional reprogramming. Transcriptional memory refers to the ability of primed plants to remember previously experienced stress and acquire enhanced tolerance to similar or different stresses. Epigenetic modifications mediate transcriptional memory and play a key role in adapting to adverse temperatures. Understanding the mechanisms of the formation, maintenance, and resetting of stress-induced transcriptional memory will not only enable us to understand why there is a trade-off between plant defense and growth, but also provide a theoretical basis for generating stress-tolerant crops optimized for future climate change. In this review, we summarize recent advances in dissecting the mechanisms of plant transcriptional memory in response to adverse temperatures, based mainly on studies of the model plant Arabidopsis thaliana. We also discuss remaining questions that are important for further understanding the mechanisms of transcriptional memory during the adverse temperature response.

Hybrid protein assembly-histone modification mechanism for PRC2-based epigenetic switching and memory

The histone modification H3K27me3 plays a central role in Polycomb-mediated epigenetic silencing. H3K27me3 recruits and allosterically activates Polycomb Repressive Complex 2 (PRC2), which adds this modification to nearby histones, providing a read/write mechanism for inheritance through DNA replication. However, for some PRC2 targets, a purely histone-based system for epigenetic inheritance may be insufficient. We address this issue at the Polycomb target FLOWERING LOCUS C (FLC) in Arabidopsis thaliana, as a narrow nucleation region of only ~three nucleosomes within FLC mediates epigenetic state switching and subsequent memory over many cell cycles. To explain the memory's unexpected persistence, we introduce a mathematical model incorporating extra protein memory storage elements with positive feedback that persist at the locus through DNA replication, in addition to histone modifications. Our hybrid model explains many features of epigenetic switching/memory at FLC and encapsulates generic mechanisms that may be widely applicable.

Digital paradigm for Polycomb epigenetic switching and memory

How epigenetic memory states are established and maintained is a central question in gene regulation. A major epigenetic process important for developmental biology involves Polycomb-mediated chromatin silencing. Significant progress has recently been made on elucidating Polycomb silencing in plant systems through analysis of Arabidopsis FLOWERING LOCUS C (FLC). Quantitative silencing of FLC by prolonged cold exposure was shown to represent an ON to OFF switch in an increasing proportion of cells. Here, we review the underlying all-or-nothing, digital paradigm for Polycomb epigenetic silencing. We then examine other Arabidopsis Polycomb-regulated targets where digital regulation may also be relevant.

Epigenetic regulation of abiotic stress memory: maintaining the good things while they last

As sessile organisms, plants have evolved sophisticated ways to constantly gauge and adapt to changing environmental conditions including extremes that may be harmful to their growth and development and are thus perceived as stress. In nature, stressful events are often chronic or recurring and thus an initial stress may prime a plant to respond more efficiently to a subsequent stress event. An epigenetic basis of such stress memory was long postulated and in recent years it has been shown that this is indeed the case. High temperature stress has proven an excellent system to unpick the molecular basis of somatic stress memory, which includes histone modifications and nucleosome occupancy. This review discusses recent findings and pinpoints open questions in the field.

Natural temperature fluctuations promote COOLAIR regulation of FLC

In this study, Zhao et al. set out to characterize how plants respond to cold through regulation of FLC expression. Using genetics and genomics approaches, the authors reveal how natural temperature fluctuations promote COOLAIR regulation of FLC, with the first autumn frost acting as a key indicator of autumn/winter arrival.

Plants monitor many aspects of their fluctuating environments to help align their development with seasons. Molecular understanding of how noisy temperature cues are registered has emerged from dissection of vernalization in Arabidopsis, which involves a multiphase cold-dependent silencing of the floral repressor locus FLOWERING LOCUS C (FLC). Cold-induced transcriptional silencing precedes a low probability PRC2 epigenetic switching mechanism. The epigenetic switch requires the absence of warm temperatures as well as long-term cold exposure. However, the natural temperature inputs into the earlier transcriptional silencing phase are less well understood. Here, through investigation of Arabidopsis accessions in natural and climatically distinct field sites, we show that the first seasonal frost strongly induces expression of COOLAIR, the antisense transcripts at FLC. Chamber experiments delivering a constant mean temperature with different fluctuations showed the freezing induction of COOLAIR correlates with stronger repression of FLC mRNA. Identification of a mutant that ectopically activates COOLAIR revealed how COOLAIR up-regulation can directly reduce FLC expression. Consistent with this, transgenes designed to knockout COOLAIR perturbed the early phase of FLC silencing. However, all transgenes designed to remove COOLAIR resulted in increased production of novel convergent FLC antisense transcripts. Our study reveals how natural temperature fluctuations promote COOLAIR regulation of FLC, with the first autumn frost acting as a key indicator of autumn/winter arrival.

Establishment of heterochromatin in domain-size-dependent bursts

Methylation of histone H3K9 is a hallmark of epigenetic silencing in eukaryotes. Nucleosome modifications often rely on positive feedback where enzymes are recruited by modified nucleosomes. A combination of local and global feedbacks has been proposed to account for some dynamic properties of heterochromatin, but the range at which the global feedbacks operate and the exact mode of heterochromatin propagation are not known. We investigated these questions in fission yeast. Guided by mathematical modeling, we incrementally increased the size of the mating-type region and profiled heterochromatin establishment over time. We observed exponential decays in the proportion of cells with active reporters, with rates that decreased with domain size. Establishment periods varied from a few generations in wild type to >200 generations in the longest region examined, and highly correlated silencing of two reporters located outside the nucleation center was observed. On a chromatin level, this indicates that individual regions are silenced in sudden bursts. Mathematical modeling accounts for these bursts if heterochromatic nucleosomes facilitate a deacetylation or methylation reaction at long range, in a distance-independent manner. A likely effector of three-dimensional interactions is the evolutionarily conserved Swi6^HP1 H3K9me reader, indicating the bursting behavior might be a general mode of heterochromatin propagation.

The Flowering Season-Meter at FLOWERING LOCUS C Across Life Histories in Crucifers

Many plant species overwinter before they flower. Transition to flowering is aligned to the seasonal transition as a response to the prolonged cold in winter by a process called vernalization. Multiple well-documented vernalization properties in crucifer species with diverse life histories are derived from environmental regulation of a central inhibitor of the flowering gene, Flowering Locus C (FLC). Episode(s) of flowering are prevented during high FLC expression and enabled during low FLC expression. FLC repression outlasts the winter to coincide with spring; this heterochronic aspect is termed "winter memory." In the annual Arabidopsis thaliana, winter memory has long been associated with the highly conserved histone modifiers Polycomb and Trithorax, which have antagonistic roles in transcription. However, there are experimental limitations in determining how dynamic, heterogenous histone modifications within the FLC locus generate the final transcriptional output. Recent theoretical considerations on cell-to-cell variability in gene expression and histone modifications generating bistable states brought support to the hypothesis of chromatin-encoded memory, as with other experimental systems in eukaryotes. Furthermore, these advances unify multiple properties of vernalization, not only the winter memory. Similarly, in the perennial Arabidopsis halleri ssp. gemmifera, recent integration of molecular with mathematical and ecological approaches unifies FLC chromatin features with the all-year-round memory of seasonal temperature. We develop the concept of FLC season-meter to combine existing information from the contrasting annual/perennial and experimental/theoretical sectors into a transitional framework. We highlight simplicity, high conservation, and discrete differences across extreme life histories in crucifers.

In search of lost time: Enhancers as modulators of timing in lymphocyte development and differentiation

Proper timing of gene expression is central to lymphocyte development and differentiation. Lymphocytes often delay gene activation for hours to days after the onset of signaling components, which act on the order of seconds to minutes. Such delays play a prominent role during the intricate choreography of developmental events and during the execution of an effector response. Though a number of mechanisms are sufficient to explain timing at short timescales, it is not known how timing delays are implemented over long timescales that may span several cell generations. Based on the literature, we propose that a class of cis-regulatory elements, termed "timing enhancers," may explain how timing delays are controlled over these long timescales. By considering chromatin as a kinetic barrier to state switching, the timing enhancer model explains experimentally observed dynamics of gene expression where other models fall short. In this review, we elaborate on features of the timing enhancer model and discuss the evidence for its generality throughout development and differentiation. We then discuss potential molecular mechanisms underlying timing enhancer function. Finally, we explore recent evidence drawing connections between timing enhancers and genetic risk for immunopathology. We argue that the timing enhancer model is a useful framework for understanding how cis-regulatory elements control the central dimension of timing in lymphocyte biology.

Using computational modelling to reveal mechanisms of epigenetic Polycomb control

The Polycomb system is essential for stable gene silencing in many organisms. This regulation is achieved in part through addition of the histone modifications H3K27me2/me3 by Polycomb Repressive Complex 2 (PRC2). These modifications are believed to be the causative epigenetic memory elements of PRC2-mediated silencing. As these marks are stored locally in the chromatin, PRC2-based memory is a cis-acting system. A key feature of stable epigenetic memory in cis is PRC2-mediated, self-reinforcing feedback from K27-methylated histones onto nearby histones in a read-write paradigm. However, it was not clear under what conditions such feedback can lead to stable memory, able, for example, to survive the perturbation of histone dilution at DNA replication. In this context, computational modelling has allowed a rigorous exploration of possible underlying memory mechanisms and has also greatly accelerated our understanding of switching between active and silenced states. Specifically, modelling has predicted that switching and memory at Polycomb loci is digital, with a locus being either active or inactive, rather than possessing intermediate, smoothly varying levels of activation. Here, we review recent advances in models of Polycomb control, focusing on models of epigenetic switching through nucleation and spreading of H3K27me2/me3. We also examine models that incorporate transcriptional feedback antagonism and those including bivalent chromatin states. With more quantitative experimental data on histone modification kinetics, as well as single-cell resolution data on transcription and protein levels for PRC2 targets, we anticipate an expanded need for modelling to help dissect increasingly interconnected and complex memory mechanisms.

Feeling Every Bit of Winter - Distributed Temperature Sensitivity in Vernalization

Temperature intrinsically influences all aspects of biochemical and biophysical processes. Organisms have therefore evolved strategies to buffer themselves against thermal perturbations. Many organisms also use temperature signals as cues to align behavior and development with certain seasons. These developmentally important thermosensory mechanisms have generally been studied in constant temperature conditions. However, environmental temperature is an inherently noisy signal, and it has been unclear how organisms reliably extract specific temperature cues from fluctuating temperature profiles. In this context, we discuss plant thermosensory responses, focusing on temperature sensing throughout vernalization in Arabidopsis. We highlight many different timescales of sensing, which has led to the proposal of a distributed thermosensing paradigm. Within this paradigm, we suggest a classification system for thermosensors. Finally, we focus on the longest timescale, which is most important for sensing winter, and examine the different mechanisms in which memory of cold exposure can be achieved.

Resetting FLOWERING LOCUS C Expression After Vernalization Is Just Activation in the Early Embryo by a Different Name

The reproductive success of many plants depends on their capacity to respond appropriately to their environment. One environmental cue that triggers flowering is the extended cold of winter, which promotes the transition from vegetative to reproductive growth in a response known as vernalization. In annual plants of the Brassicaceae, the floral repressor, FLOWERING LOCUS C (FLC), is downregulated by exposure to low temperatures. Repression is initiated during winter cold and then maintained as the temperature rises, allowing plants to complete their life cycle during spring and summer. The two stages of FLC repression, initiation and maintenance, are distinguished by different chromatin states at the FLC locus. Initiation involves the removal of active chromatin marks and the deposition of the repressive mark H3K27me3 over a few nucleosomes in the initiation zone, also known as the nucleation region. H3K27me3 then spreads to cover the entire locus, in a replication dependent manner, to maintain FLC repression. FLC is released from repression in the next generation, allowing progeny of a vernalized plant to respond to winter. Activation of FLC in this generation has been termed resetting to denote the restoration of the pre-vernalized state in the progeny of a vernalized plant. It has been assumed that resetting must differ from the activation of FLC expression in progeny of plants that have not experienced winter cold. Considering that there is now strong evidence indicating that chromatin undergoes major modifications during both male and female gametogenesis, it is time to challenge this assumption.

[Developmental plasticity in plants: an interaction between hormones and epigenetics at the meristem level]

Plants are fixed organisms with continuous development throughout their life and great sensitivity to environmental variations. They react in this way by exhibiting large developmental phenotypic plasticity. This plasticity is partly controlled by (phyto)hormones, but recent studies also suggest the involvement of epigenetic mechanisms. It seems that these two factors may interact in a complex way and especially in the stem cells grouped together in meristems. The objective of this review is to present the current arguments about this interaction which would promote developmental plasticity. Three major points are thus addressed to justify this interaction between hormonal control and epigenetics (control at the chromatin level) for the developmental plasticity of plants: the arguments in favor of an effect of hormones on chromatin and vice versa, the arguments in favor of their roles on developmental plasticity and finally the arguments in favor of the central place of these interactions, the meristems. Various perspectives and applications are discussed.

Epigenomic Reprogramming as a Driver of Malignant Glioma

Malignant gliomas are central nervous system tumors and remain among the most treatment-resistant cancers. Exome sequencing has revealed significant heterogeneity and important insights into the molecular pathogenesis of gliomas. Mutations in chromatin modifiers-proteins that shape the epigenomic landscape through remodeling and regulation of post-translational modifications on chromatin-are very frequent and often define specific glioma subtypes. This suggests that epigenomic reprogramming may be a fundamental driver of glioma. Here, we describe the key chromatin regulatory pathways disrupted in gliomas, delineating their physiological function and our current understanding of how their dysregulation may contribute to gliomagenesis.

The Arabidopsis epigenetic regulator ICU11 as an accessory protein of Polycomb Repressive Complex 2

Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states.

Unique and contrasting effects of light and temperature cues on plant transcriptional programs

Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression in response to stress or to drive developmental transitions. Among the many signals that plants perceive, light and temperature are of particular interest due to their intensely fluctuating nature which is combined with a long-term seasonal trend. Whereas specific receptors are key in the light-sensing mechanism, the identity of plant thermosensors for high and low temperatures remains far from fully addressed. This review aims at discussing common as well as divergent characteristics of gene expression regulation in plants, controlled by light and temperature. Light and temperature signaling control the abundance of specific transcription factors, as well as the dynamics of co-transcriptional processes such as RNA polymerase elongation rate and alternative splicing patterns. Additionally, sensing both types of cues modulates gene expression by altering the chromatin landscape and through the induction of long non-coding RNAs (lncRNAs). However, while light sensing is channeled through dedicated receptors, temperature can broadly affect chemical reactions inside plant cells. Thus, direct thermal modifications of the transcriptional machinery add another level of complexity to plant transcriptional regulation. Besides the rapid transcriptome changes that follow perception of environmental signals, plant developmental transitions and acquisition of stress tolerance depend on long-term maintenance of transcriptional states (active or silenced genes). Thus, the rapid transcriptional response to the signal (Phase I) can be distinguished from the long-term memory of the acquired transcriptional state (Phase II - remembering the signal). In this review we discuss recent advances in light and temperature signal perception, integration and memory in Arabidopsis thaliana, focusing on transcriptional regulation and highlighting the contrasting and unique features of each type of cue in the process.

Repressive chromatin modification underpins the long-term expression trend of a perennial flowering gene in nature

Natural environments require organisms to possess robust mechanisms allowing responses to seasonal trends. In Arabidopsis halleri, the flowering regulator AhgFLC shows upregulation and downregulation phases along with long-term past temperature, but the underlying machinery remains elusive. Here, we investigate the seasonal dynamics of histone modifications, H3K27me3 and H3K4me3, at AhgFLC in a natural population. Our advanced modelling and transplant experiments reveal that H3K27me3-mediated chromatin regulation at AhgFLC provides two essential properties. One is the ability to respond to the long-term temperature trends via bidirectional interactions between H3K27me3 and H3K4me3; the other is the ratchet-like character of the AhgFLC system, i.e. reversible in the entire perennial life cycle but irreversible during the upregulation phase. Furthermore, we show that the long-term temperature trends are locally indexed at AhgFLC in the form of histone modifications. Our study provides a more comprehensive understanding of H3K27me3 function at AhgFLC in a complex natural environment.

The flowering regulator FLC shows upregulation and downregulation phases along with long-term past temperature in Arabidopsishalleri. Here, the authors reveal that H3K27me3-mediated chromatin regulation at AhgFLC provides the ability to respond to both the seasonal temperature trends and the perennial life cycle.

Noncoding SNPs influence a distinct phase of Polycomb silencing to destabilize long-term epigenetic memory at Arabidopsis FLC

In Arabidopsis thaliana, the cold-induced epigenetic regulation of FLOWERING LOCUS C (FLC) involves distinct phases of Polycomb repressive complex 2 (PRC2) silencing. During cold, a PHD-PRC2 complex metastably and digitally nucleates H3K27me3 within FLC On return to warm, PHD-PRC2 spreads across the locus delivering H3K27me3 to maintain long-term silencing. Here, we studied natural variation in this process in Arabidopsis accessions, exploring Lov-1, which shows FLC reactivation on return to warm, a feature characteristic of FLC in perennial Brassicaceae This analysis identifies an additional phase in this Polycomb silencing mechanism downstream from H3K27me3 spreading. In this long-term silencing (perpetuated) phase, the PHD proteins are lost from the nucleation region and silencing is likely maintained by the read-write feedbacks associated with H3K27me3. A combination of noncoding SNPs in the nucleation region mediates instability in this long-term silencing phase with the result that Lov-1 FLC frequently digitally reactivates in individual cells, with a probability that diminishes with increasing cold duration. We propose that this decrease in reactivation probability is due to reduced DNA replication after flowering. Overall, this work defines an additional phase in the Polycomb mechanism instrumental in natural variation of silencing, and provides avenues to dissect broader evolutionary changes at FLC.

Epigenetic memory independent of symmetric histone inheritance

Heterochromatic gene silencing is an important form of gene regulation that usually requires specific histone modifications. A popular model posits that inheritance of modified histones, especially in the form of H3-H4 tetramers, underlies inheritance of heterochromatin. Because H3-H4 tetramers are randomly distributed between daughter chromatids during DNA replication, rare occurrences of asymmetric tetramer inheritance within a heterochromatic domain would have the potential to destabilize heterochromatin. This model makes a prediction that shorter heterochromatic domains would experience unbalanced tetramer inheritance more frequently, and thereby be less stable. In contrast to this prediction, we found that shortening a heterochromatic domain in Saccharomyces had no impact on the strength of silencing nor its heritability. Additionally, we found that replisome mutations that disrupt inheritance of H3-H4 tetramers had only minor effects on heterochromatin stability. These findings suggest that histones carry little or no memory of the heterochromatin state through DNA replication.

A crucial process in life is the ability of cells to pass on useful information to their descendants. Some of this information is encoded within molecules of DNA, including genes that contain specific coded instructions. Another layer of information helps to specify whether individual genes are switched on or off, which means cells with the same genes can perform different tasks. However, it remains unclear exactly how cells pass on this additional layer of “epigenetic” information.

Inside human, yeast and other eukaryotic cells, DNA is wrapped around scaffold proteins known as histones. Cells modify histones by adding chemical tags to them, and histones within the same gene often have specific patterns of chemical tags. One popular hypothesis is that these marked histones constitute epigenetic information that may be passed on when DNA replicates before a cell divides to make two daughter cells. This model predicts that the marked histones need to be divided equally between the two sets of DNA to allow the epigenetic information to be faithfully passed on to both daughter cells.

To test this prediction, Saxton and Rine studied a gene called HMR that is involved in mating in yeast. This gene is constantly silenced (in other words, not actively providing instructions to the cell) and contains histones with very specific patterns of chemical tags. For the experiments, Saxton and Rine made a series of mutations in the yeast that increased how often these marked histones were divided unequally when the yeast cells replicated their DNA. Unexpectedly, these mutations had little impact on the ability of the cells to pass on the silenced state of HMR to their offspring. These findings argue against the classic model that marked histones carry epigenetic information.

Storing memories: the distinct phases of Polycomb-mediated silencing of Arabidopsis FLC

Polycomb-mediated epigenetic silencing is central to correct growth and development in higher eukaryotes. The evolutionarily conserved Polycomb repressive complex 2 (PRC2) transcriptionally silences target genes through a mechanism requiring the histone modification H3K27me3. However, we still do not fully understand what defines Polycomb targets, how their expression state is switched from epigenetically ON to OFF and how silencing is subsequently maintained through many cell divisions. An excellent system in which to dissect the sequence of events underlying an epigenetic switch is the Arabidopsis FLC locus. Exposure to cold temperatures progressively induces a PRC2-dependent switch in an increasing proportion of cells, through a mechanism that is driven by the local chromatin environment. Temporally distinct phases of this silencing mechanism have been identified. First, the locus is transcriptionally silenced in a process involving cold-induced antisense transcripts; second, nucleation at the first exon/intron boundary of a Polycomb complex containing cold-induced accessory proteins induces a metastable epigenetically silenced state; third, a Polycomb complex with a distinct composition spreads across the locus in a process requiring DNA replication to deliver long-term epigenetic silencing. Detailed understanding from this system is likely to provide mechanistic insights important for epigenetic silencing in eukaryotes generally.

Theoretical analysis of Polycomb-Trithorax systems predicts that poised chromatin is bistable and not bivalent

Polycomb (PcG) and Trithorax (TrxG) group proteins give stable epigenetic memory of silent and active gene expression states, but also allow poised states in pluripotent cells. Here we systematically address the relationship between poised, active and silent chromatin, by integrating 73 publications on PcG/TrxG biochemistry into a mathematical model comprising 144 nucleosome modification states and 8 enzymatic reactions. Our model predicts that poised chromatin is bistable and not bivalent. Bivalent chromatin, containing opposing active and silent modifications, is present as an unstable background population in all system states, and different subtypes co-occur with active and silent chromatin. In contrast, bistability, in which the system switches frequently between stable active and silent states, occurs under a wide range of conditions at the transition between monostable active and silent system states. By proposing that bistability and not bivalency is associated with poised chromatin, this work has implications for understanding the molecular nature of pluripotency.

Polycomb and Trithorax group proteins regulate silent and active gene expression states, but also allow poised states in pluripotent cells. Here the authors present a mathematical model that integrates data on Polycomb/ Trithorax biochemistry into a single coherent framework which predicts that poised chromatin is not bivalent as previously proposed, but is bistable, meaning that the system switches frequently between stable active and silent states.

Temperature Sensing Is Distributed throughout the Regulatory Network that Controls FLC Epigenetic Silencing in Vernalization

Many organisms need to respond to complex, noisy environmental signals for developmental decision making. Here, we dissect how Arabidopsis plants integrate widely fluctuating field temperatures over month-long timescales to progressively upregulate VERNALIZATION INSENSITIVE3 (VIN3) and silence FLOWERING LOCUS C (FLC), aligning flowering with spring. We develop a mathematical model for vernalization that operates on multiple timescales-long term (month), short term (day), and current (hour)-and is constrained by experimental data. Our analysis demonstrates that temperature sensing is not localized to specific nodes within the FLC network. Instead, temperature sensing is broadly distributed, with each thermosensory process responding to specific features of the plants' history of exposure to warm and cold. The model accurately predicts FLC silencing in new field data, allowing us to forecast FLC expression in changing climates. We suggest that distributed thermosensing may be a general property of thermoresponsive regulatory networks in complex natural environments.

Remembering winter through vernalisation

Vernalisation is the programmed physiological process in which prolonged cold-exposure provides competency to flower in plants; widely found in winter and biennial species, such as Arabidopsis, fruit trees, vegetables and wheat. This phenomenon is regulated by diverse genetic networks, and memory of vernalisation in a life cycle mainly depends on epigenetic mechanisms. However, less is known about how to count winter-dosage for flowering in plants. Here, we compare the vernalisation genetic framework between the dicots Arabidopsis, temperate grasses, wheat, barley and Brachypodium. We discuss vernalisation mechanisms involving crosstalk between phosphorylation and O-GlcNAcylation modification of key proteins, and epigenetic modifications of the key gene VRN1 in wheat. We also highlight the potential evolutionary origins of vernalisation in various species. Current progress toward understanding the regulation of vernalisation requirements provides insight that will inform the design of molecular breeding strategies for winter crops.

A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment

Cell fate decisions occur through the switch-like, irreversible activation of fate-specifying genes. These activation events are often assumed to be tightly coupled to changes in upstream transcription factors, but could also be constrained by cis-epigenetic mechanisms at individual gene loci. Here, we studied the activation of Bcl11b, which controls T-cell fate commitment. To disentangle cis and trans effects, we generated mice where two Bcl11b copies are tagged with distinguishable fluorescent proteins. Quantitative live microscopy of progenitors from these mice revealed that Bcl11b turned on after a stochastic delay averaging multiple days, which varied not only between cells but also between Bcl11b alleles within the same cell. Genetic perturbations, together with mathematical modeling, showed that a distal enhancer controls the rate of epigenetic activation, while a parallel Notch-dependent trans-acting step stimulates expression from activated loci. These results show that developmental fate transitions can be controlled by stochastic cis-acting events on individual loci.

The seekers: how epigenetic modifying enzymes find their hidden genomic targets in Arabidopsis

Epigenetic regulation plays fundamental roles in modulating chromatin-based processes and shaping the epigenome in multicellular eukaryotes, including plants. How epigenetic factors recognize their target loci hiding in the vast genomic DNA sequence remains a long-standing mystery. During the past several years, a growing body of work has revealed the complex, dynamic, and diverse chromatin-targeting mechanisms of these epigenetic factors. In this review, we focus on recent advances in understanding the recruitment of epigenetic factors to specific genomic regions, based on data from Arabidopsis thaliana.

Epigenetic Environmental Memories in Plants: Establishment, Maintenance, and Reprogramming

Plants are immobile and must respond to or endure fluctuating surroundings and diverse environmental challenges. Environmental inputs often induce chromatin modifications at various responsive genes and consequent changes in their expression. Environment-induced chromatin marks at certain loci are transmittable through cell divisions after relief from the original external signals, leading to acquired 'memorization' of environmental experiences in plants, namely epigenetic environmental memories, which enable plants to adapt to environmental changes or to perform better when events recur. Here, we review recent progress in epigenetic or chromatin-mediated environmental memories in plants, including defense priming, stress memories, and 'epigenetic memory of winter cold' or vernalization. Various advances in epigenetic mechanisms underlying plant-environment interactions highlight that plant environmental epigenetics is emerging as an important area in plant biology.

Array of MADS-Box Genes: Facilitator for Rapid Adaptation?

In a world of global warming, the question emerges whether all plants have suitable mechanisms to keep pace with the rapidly changing environment. Most previous studies have focused on either the ability of plants to rapidly acclimatize via physiological and developmental plasticity, or long-term adaptation over thousands of years. However, we wonder whether plants can also adapt to changes in the environment within only a few generations. We hypothesize that rapidly evolving clusters of tandemly duplicated developmental control genes represent a source for fast adaptation. Specifically, we propose that a tandem cluster of FLC-like MADS-box genes involved in the transition to flowering in Arabidopsis functions as a facilitator for rapid adaptation to changes in ambient temperature.

Ten principles of heterochromatin formation and function

Heterochromatin is a key architectural feature of eukaryotic chromosomes, which endows particular genomic domains with specific functional properties. The capacity of heterochromatin to restrain the activity of mobile elements, isolate DNA repair in repetitive regions and ensure accurate chromosome segregation is crucial for maintaining genomic stability. Nucleosomes at heterochromatin regions display histone post-translational modifications that contribute to developmental regulation by restricting lineage-specific gene expression. The mechanisms of heterochromatin establishment and of heterochromatin maintenance are separable and involve the ability of sequence-specific factors bound to nascent transcripts to recruit chromatin-modifying enzymes. Heterochromatin can spread along the chromatin from nucleation sites. The propensity of heterochromatin to promote its own spreading and inheritance is counteracted by inhibitory factors. Because of its importance for chromosome function, heterochromatin has key roles in the pathogenesis of various human diseases. In this Review, we discuss conserved principles of heterochromatin formation and function using selected examples from studies of a range of eukaryotes, from yeast to human, with an emphasis on insights obtained from unicellular model organisms.

Frequency Modulation of Transcriptional Bursting Enables Sensitive and Rapid Gene Regulation

Gene regulation is a complex non-equilibrium process. Here, we show that quantitating the temporal regulation of key gene states (transcriptionally inactive, active, and refractory) provides a parsimonious framework for analyzing gene regulation. Our theory makes two non-intuitive predictions. First, for transcription factors (TFs) that regulate transcription burst frequency, as opposed to amplitude or duration, weak TF binding is sufficient to elicit strong transcriptional responses. Second, refractoriness of a gene after a transcription burst enables rapid responses to stimuli. We validate both predictions experimentally by exploiting the natural, optogenetic-like responsiveness of the Neurospora GATA-type TF White Collar Complex (WCC) to blue light. Further, we demonstrate that differential regulation of WCC target genes is caused by different gene activation rates, not different TF occupancy, and that these rates are tuned by both the core promoter and the distance between TF-binding site and core promoter. In total, our work demonstrates the relevance of a kinetic, non-equilibrium framework for understanding transcriptional regulation.

Shaping epigenetic memory via genomic bookmarking

Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and maintain robust yet plastic epigenetic domains via genomic bookmarking (GBM). We model chromatin as a recolourable polymer whose segments bear non-permanent histone marks (or colours) which can be modified by 'writer' proteins. The three-dimensional chromatin organisation is mediated by protein bridges, or 'readers', such as Polycomb Repressive Complexes and Transcription Factors. The coupling between readers and writers drives spreading of biochemical marks and sustains the memory of local chromatin states across replication and mitosis. In contrast, GBM-targeted perturbations destabilise the epigenetic patterns. Strikingly, we demonstrate that GBM alone can explain the full distribution of Polycomb marks in a whole Drosophila chromosome. We finally suggest that our model provides a starting point for an understanding of the biophysics of cellular differentiation and reprogramming.

RNA Immunoprecipitation Protocol to Identify Protein-RNA Interactions in Arabidopsis thaliana

The role of RNA-binding proteins in the regulation of epigenetic processes has received increasing attention in the past decades. In particular noncoding RNAs have been shown to play a role in chromatin loop formation, recruitment of chromatin modifiers and RNA-dependent DNA methylation. In plants, the identification of specific RNA-protein interactions is now rising, facilitated by the development of specific approaches for plant tissues. Here, we present a simple one-day RNA immunoprecipitation (RIP) protocol adapted for Arabidopsis, suited for the identification of RNAs that are associated with a protein-of-interest in planta.