Remembering the prolonged cold of winter

Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M

Plants integrate seasonal cues such as temperature and day length to optimally adjust their flowering time to the environment. Compared to the control of flowering before and after winter by the vernalization and day length pathways, mechanisms that delay or promote flowering during a transient cool or warm period, especially during spring, are less well understood. Due to global warming, understanding this ambient temperature pathway has gained increasing importance. In Arabidopsis thaliana, FLOWERING LOCUS M (FLM) is a critical flowering regulator of the ambient temperature pathway. FLM is alternatively spliced in a temperature-dependent manner and the two predominant splice variants, FLM-ß and FLM-δ, can repress and activate flowering in the genetic background of the A. thaliana reference accession Columbia-0. The relevance of this regulatory mechanism for the environmental adaptation across the entire range of the species is, however, unknown. Here, we identify insertion polymorphisms in the first intron of FLM as causative for accelerated flowering in many natural A. thaliana accessions, especially in cool (15°C) temperatures. We present evidence for a potential adaptive role of this structural variation and link it specifically to changes in the abundance of FLM-ß. Our results may allow predicting flowering in response to ambient temperatures in the Brassicaceae.

Binary Switching of Calendar Cells in the Pituitary Defines the Phase of the Circannual Cycle in Mammals

Persistent free-running circannual (approximately year-long) rhythms have evolved in animals to regulate hormone cycles, drive metabolic rhythms (including hibernation), and time annual reproduction. Recent studies have defined the photoperiodic input to this rhythm, wherein melatonin acts on thyrotroph cells of the pituitary pars tuberalis (PT), leading to seasonal changes in the control of thyroid hormone metabolism in the hypothalamus. However, seasonal rhythms persist in constant conditions in many species in the absence of a changing photoperiod signal, leading to the generation of circannual cycles. It is not known which cells, tissues, and pathways generate these remarkable long-term rhythmic processes. We show that individual PT thyrotrophs can be in one of two binary states reflecting either a long (EYA3(+)) or short (CHGA(+)) photoperiod, with the relative proportion in each state defining the phase of the circannual cycle. We also show that a morphogenic cycle driven by the PT leads to extensive re-modeling of the PT and hypothalamus over the circannual cycle. We propose that the PT may employ a recapitulated developmental pathway to drive changes in morphology of tissues and cells. Our data are consistent with the hypothesis that the circannual timer may reside within the PT thyrotroph and is encoded by a binary switch timing mechanism, which may regulate the generation of circannual neuroendocrine rhythms, leading to dynamic re-modeling of the hypothalamic interface. In summary, the PT-ventral hypothalamus now appears to be a prime structure involved in long-term rhythm generation.

Transcriptional programs regulated by both LEAFY and APETALA1 at the time of flower formation

Two key regulators of the switch to flower formation and of flower patterning in Arabidopsis are the plant-specific helix-turn-helix transcription factor LEAFY (LFY) and the MADS box transcription factor APETALA1 (AP1). The interactions between these two transcriptional regulators are complex. AP1 is both a direct target of LFY and can act in parallel with LFY. Available genetic and molecular evidence suggests that LFY and AP1 together orchestrate the switch to flower formation and early events during flower morphogenesis by altering transcriptional programs. However, very little is known about target genes regulated by both transcription factors. Here, we performed a meta-analysis of public datasets to identify genes that are likely to be regulated by both LFY and AP1. Our analyses uncovered known and novel direct LFY and AP1 targets with a role in the control of onset of flower formation. It also identified additional families of proteins and regulatory pathways that may be under transcriptional control by both transcription factors. In particular, several of these genes are linked to response to hormones, to transport and to development. Finally, we show that the gibberellin catabolism enzyme ELA1, which was recently shown to be important for the timing of the switch to flower formation, is positively feedback-regulated by AP1. Our study contributes to the elucidation of the regulatory network that leads to formation of a vital plant organ system, the flower.

Flowering Locus C's Lessons: Conserved Chromatin Switches Underpinning Developmental Timing and Adaptation

Analysis of how seasonal cues influence the timing of the floral transition has revealed many important principles for how epigenetic regulation can integrate a variety of environmental cues with developmental signals. The study of the pathways that necessitate overwintering in plants and their ability to respond to prolonged cold (the vernalization requirement and response pathways) has elaborated different chromatin regulatory pathways and the involvement of noncoding RNAs. The major target of these vernalization pathways in Arabidopsis (Arabidopsis thaliana) is Flowering Locus C (FLC). A relatively simple picture of FLC regulation is emerging of a few core complexes and mechanisms that antagonize each other's actions. This balance provides a fine degree of control that has nevertheless permitted evolution of a wide range of natural variation in vernalization in Arabidopsis. Similar simple routes of adaptation may underlie life history variation between species.

MAF2 Is Regulated by Temperature-Dependent Splicing and Represses Flowering at Low Temperatures in Parallel with FLM

Plants enter their reproductive phase when the environmental conditions are favourable for the successful production of progeny. The transition from vegetative to reproductive phase is influenced by several environmental factors including ambient temperature. In the model plant Arabidopsis thaliana, SHORT VEGETATIVE PHASE (SVP) is critical for this pathway; svp mutants cannot modify their flowering time in response to ambient temperature. SVP encodes a MADS-box transcription factor that directly represses genes that promote flowering. SVP binds DNA in complexes with other MADS-box transcription factors, including FLOWERING LOCUS M (FLM), which acts with SVP to repress the floral transition at low temperatures. Small temperature changes post-transcriptionally regulate FLM through temperature-dependent alternative splicing (TD-AS). As ambient temperature increases, the predominant FLM splice isoform shifts to encode a protein incapable of exerting a repressive effect on flowering. Here we characterize a closely related MADS-box transcription factor, MADS AFFECTING FLOWERING2 (MAF2), which has independently evolved TD-AS. At low temperatures the most abundant MAF2 splice variant encodes a protein that interacts with SVP to repress flowering. At increased temperature the relative abundance of splice isoforms shifts in favour of an intron-retaining variant that introduces a premature termination codon. We show that this isoform encodes a protein that cannot interact with SVP or repress flowering. At lower temperatures MAF2 and SVP repress flowering in parallel with FLM and SVP, providing an additional input to sense ambient temperature for the control of flowering.

Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution

Environment has a critical role in the natural selection process for Darwinian evolution. The primary molecular component currently considered for neo-Darwinian evolution involves genetic alterations and random mutations that generate the phenotypic variation required for natural selection to act. The vast majority of environmental factors cannot directly alter DNA sequence. Epigenetic mechanisms directly regulate genetic processes and can be dramatically altered by environmental factors. Therefore, environmental epigenetics provides a molecular mechanism to directly alter phenotypic variation generationally. Lamarck proposed in 1802 the concept that environment can directly alter phenotype in a heritable manner. Environmental epigenetics and epigenetic transgenerational inheritance provide molecular mechanisms for this process. Therefore, environment can on a molecular level influence the phenotypic variation directly. The ability of environmental epigenetics to alter phenotypic and genotypic variation directly can significantly impact natural selection. Neo-Lamarckian concept can facilitate neo-Darwinian evolution. A unified theory of evolution is presented to describe the integration of environmental epigenetic and genetic aspects of evolution.

PcG and trxG in plants - friends or foes

The highly-conserved Polycomb group (PcG) and trithorax group (trxG) proteins play major roles in regulating gene expression and maintaining developmental states in many organisms. However, neither the recruitment of Polycomb repressive complexes (PRC) nor the mechanisms of PcG and trxG-mediated gene silencing and activation are well understood. Recent progress in Arabidopsis research challenges the dominant model of PRC2-dependent recruitment of PRC1 to target genes. Moreover, evidence indicates that diverse forms of PRC1, with shared components, are a common theme in plants and mammals. Although trxG is known to antagonize PcG, emerging data reveal that trxG can also repress gene expression, acting cooperatively with PcG. We discuss these recent findings and highlight the employment of diverse epigenetic mechanisms during development in plants and animals.

Adaptation to the local environment by modifications of the photoperiod response in crops

Flowering plants produce a meristem at the shoot tip where specialized tissue generates shoot apical meristems at the appropriate time to differentiate into reproductive structures, pollinate and efficiently generate seeds. The complex set of molecular and phenological events culminating in development of a flowering meristem is referred to as 'flowering time'. Flowering time affects plant productivity because plants dedicate energy to produce flowers and seeds rather than vegetative tissue once the molecular decision to initiate flowering has been taken. Thus, initiation of flowering time is an important decision in plants, especially in annual plants including crops. Humans have introduced crops into latitudes and climate areas far from their origin or natural ecosystem, requiring in many cases modification of native flowering times. Recent molecular-genetic studies shed light on the genetic basis related to such introductions. In this review, recent progress regarding crop introductions and their genetic bases are summarized, as well as the potential of other agricultural plants to be introduced into different climatic zones.

Polycomb repression in the regulation of growth and development in Arabidopsis

Chromatin state is critical for cell identity and development in multicellular eukaryotes. Among the regulators of chromatin state, Polycomb group (PcG) proteins stand out because of their role in both establishment and maintenance of cell identity. PcG proteins act in two major complexes in metazoans and plants. These complexes function to epigenetically-in a mitotically heritable manner-prevent expression of important developmental regulators at the wrong stage of development or in the wrong tissue. In Arabidopsis, PcG function is required throughout the life cycle from seed germination to embryo formation. Recent studies have expanded our knowledge regarding the biological roles and the regulation of the activity of PcG complexes. In this review, we discuss novel functions of Polycomb repression in plant development as well as advances in understanding PcG complex recruitment, activity regulation and removal in Arabidopsis and other plant species.

How is FLC repression initiated by cold?

Vernalization is the promotion of flowering in response to prolonged exposure to low temperatures. In Arabidopsis, FLOWERING LOCUS C (FLC), a suppressor of flowering, is repressed by low temperatures but the mechanism leading to the initial decrease in FLC transcription remains a mystery. No mutants that block the repression of FLC at low temperatures have been identified to date. If the failure to identify such a mutant is assumed to imply that no such mutant exists, then it follows that the first response to the drop in temperature is physical, not genetic. In this Opinion article we propose that the drop in temperature first causes a simple change in the topology of the chromatin polymer, which in turn initiates the repression of FLC transcription.

Time to flower: interplay between photoperiod and the circadian clock

Plants precisely time the onset of flowering to ensure reproductive success. A major factor in seasonal control of flowering time is the photoperiod. The length of the daily light period is measured by the circadian clock in leaves, and a signal is conveyed to the shoot apex to initiate floral transition accordingly. In the last two decades, the molecular players in the photoperiodic pathway have been identified in Arabidopsis thaliana. Moreover, the intricate connections between the circadian clockwork and components of the photoperiodic pathway have been unravelled. In particular, the molecular basis of time-of-day-dependent sensitivity to floral stimuli, as predicted by Bünning and Pittendrigh, has been elucidated. This review covers recent insights into the molecular mechanisms underlying clock regulation of photoperiodic responses and the integration of the photoperiodic pathway into the flowering time network in Arabidopsis. Furthermore, examples of conservation and divergence in photoperiodic flower induction in other plant species are discussed.

Heat can erase epigenetic marks of vernalization in Arabidopsis

Vernalization establishes a memory of winter that must be maintained for weeks or months in order to promote flowering the following spring. The stability of the vernalized state varies among plant species and depends on the duration of cold exposure. In Arabidopsis thaliana, winter leads to epigenetic silencing of the floral repressor gene FLOWERING LOCUS C (FLC) and the duration of cold is measured through the dynamics of chromatin modifications during and after cold. The growing conditions encountered post-vernalization are thus critical for the maintenance of the vernalized state. We reported that high temperature leads to devernalization and, consistently, to FLC reactivation in Arabidopsis seedlings. Here we show that the repressive epigenetic mark H3K27me3 decreases at the FLC locus when vernalized seedlings are grown at 30°C, unless they were first exposed to a stabilizing period at 20°C. Ambient temperature thus controls the epigenetic memory of winter.

PHDs govern plant development

Posttranslational modifications present in the amino-terminal tails of histones play a pivotal role in the chromatin-mediated regulation of gene expression patterns that control plant developmental transitions. Therefore, the function of protein domains that specifically recognize these histone covalent modifications and recruit chromatin remodeling complexes and the transcriptional machinery to modulate gene expression is essential for a proper control of plant development. Plant HomeoDomain (PHD) motifs act as effectors that can specifically bind a number of histone modifications and mediate the activation or repression of underlying genes. In this review we summarize recent findings that emphasize the crucial role of this versatile family of chromatin "reader" domains in the transcriptional regulation of plant developmental processes such as meiosis and postmeiotic events during pollen maturation, embryo meristem initiation and root development, germination as well as flowering time.

Dicer and Hsp104 function in a negative feedback loop to confer robustness to environmental stress

Epigenetic mechanisms can be influenced by environmental cues and thus evoke phenotypic variation. This plasticity can be advantageous for adaptation but also detrimental if not tightly controlled. Although having attracted considerable interest, it remains largely unknown if and how environmental cues such as temperature trigger epigenetic alterations. Using fission yeast, we demonstrate that environmentally induced discontinuous phenotypic variation is buffered by a negative feedback loop that involves the RNase Dicer and the protein disaggregase Hsp104. In the absence of Hsp104, Dicer accumulates in cytoplasmic inclusions and heterochromatin becomes unstable at elevated temperatures, an epigenetic state inherited for many cell divisions after the heat stress. Loss of Dicer leads to toxic aggregation of an exogenous prionogenic protein. Our results highlight the importance of feedback regulation in building epigenetic memory and uncover Hsp104 and Dicer as homeostatic controllers that buffer environmentally induced stochastic epigenetic variation and toxic aggregation of prionogenic proteins.

Endocrine disruptor induction of epigenetic transgenerational inheritance of disease

Environmental exposures such as toxicants, nutrition and stress have been shown to promote the epigenetic transgenerational inheritance of disease susceptibility. Endocrine disruptors are one of the largest groups of specific toxicants shown to promote this form of epigenetic inheritance. These environmental compounds that interfere with normal endocrine signaling are one of the largest classes of toxicants we are exposed to on a daily level. The ability of ancestral exposures to promote disease susceptibility significantly increases the potential biohazards of these toxicants. Therefore, what your great-grandmother was exposed to during pregnancy may influence your disease development, even in the absence of any exposure, and you are going to pass this on to your grandchildren. This non-genetic form of inheritance significantly impacts our understanding of biology from the origins of disease to evolutionary biology. The current review will describe the previous studies and endocrine disruptors shown to promote the epigenetic transgenerational inheritance of disease.

The roles of protein expression in synaptic plasticity and memory consolidation

The amount and availability of proteins are regulated by their synthesis, degradation, and transport. These processes can specifically, locally, and temporally regulate a protein or a population of proteins, thus affecting numerous biological processes in health and disease states. Accordingly, malfunction in the processes of protein turnover and localization underlies different neuronal diseases. However, as early as a century ago, it was recognized that there is a specific need for normal macromolecular synthesis in a specific fragment of the learning process, memory consolidation, which takes place minutes to hours following acquisition. Memory consolidation is the process by which fragile short-term memory is converted into stable long-term memory. It is accepted today that synaptic plasticity is a cellular mechanism of learning and memory processes. Interestingly, similar molecular mechanisms subserve both memory and synaptic plasticity consolidation. In this review, we survey the current view on the connection between memory consolidation processes and proteostasis, i.e., maintaining the protein contents at the neuron and the synapse. In addition, we describe the technical obstacles and possible new methods to determine neuronal proteostasis of synaptic function and better explain the process of memory and synaptic plasticity consolidation.

Epigenetic memory for stress response and adaptation in plants

In contrast to the majority of animal species, plants are sessile organisms and are, therefore, constantly challenged by environmental perturbations. Over the past few decades, our knowledge of how plants perceive environmental stimuli has increased considerably, e.g. the mechanisms for transducing environmental stress stimuli into cellular signaling cascades and gene transcription networks. In addition, it has recently been shown that plants can remember past environmental events and can use these memories to aid responses when these events recur. In this mini review, we focus on recent progress in determination of the epigenetic mechanisms used by plants under various environmental stresses. Epigenetic mechanisms are now known to play a vital role in the control of gene expression through small RNAs, histone modifications and DNA methylation. These are inherited through mitotic cell divisions and, in some cases, can be transmitted to the next generation. They therefore offer a possible mechanism for stress memories in plants. Recent studies have yielded evidence indicating that epigenetic mechanisms are indeed essential for stress memories and adaptation in plants.

Chromatin-dependent repression of the Arabidopsis floral integrator genes involves plant specific PHD-containing proteins

The interplay among histone modifications modulates the expression of master regulatory genes in development. Chromatin effector proteins bind histone modifications and translate the epigenetic status into gene expression patterns that control development. Here, we show that two Arabidopsis thaliana paralogs encoding plant-specific proteins with a plant homeodomain (PHD) motif, SHORT LIFE (SHL) and EARLY BOLTING IN SHORT DAYS (EBS), function in the chromatin-mediated repression of floral initiation and play independent roles in the control of genes regulating flowering. Previous results showed that repression of the floral integrator FLOWERING LOCUS T (FT) requires EBS. We establish that SHL is necessary to negatively regulate the expression of SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1), another floral integrator. SHL and EBS recognize di- and trimethylated histone H3 at lysine 4 and bind regulatory regions of SOC1 and FT, respectively. These PHD proteins maintain an inactive chromatin conformation in SOC1 and FT by preventing high levels of H3 acetylation, bind HISTONE DEACETYLASE6, and play a central role in regulating flowering time. SHL and EBS are widely conserved in plants but are absent in other eukaryotes, suggesting that the regulatory module mediated by these proteins could represent a distinct mechanism for gene expression control in plants.

Footprints of the sun: memory of UV and light stress in plants

Sunlight provides the necessary energy for plant growth via photosynthesis but high light and particular its integral ultraviolet (UV) part causes stress potentially leading to serious damage to DNA, proteins, and other cellular components. Plants show adaptation to environmental stresses, sometimes referred to as "plant memory." There is growing evidence that plants memorize exposure to biotic or abiotic stresses through epigenetic mechanisms at the cellular level. UV target genes such as CHALCONE SYNTHASE (CHS) respond immediately to UV treatment and studies of the recently identified UV-B receptor UV RESISTANCE LOCUS 8 (UVR8) confirm the expedite nature of UV signaling. Considering these findings, an UV memory seems redundant. However, several lines of evidence suggest that plants may develop an epigenetic memory of UV and light stress, but in comparison to other abiotic stresses there has been relatively little investigation. Here we summarize the state of knowledge about acclimation and adaptation of plants to UV light and discuss the possibility of chromatin based epigenetic memory.

Regulation of flowering time by the miR156-mediated age pathway

Precise flowering time is critical to reproductive success. In response to diverse exogenous and endogenous cues including age, hormones, photoperiod, and temperature, the floral transition is controlled by a complex regulatory network, which involves extensive crosstalks, feedback, or feedforward loops between the components within flowering time pathways. The newly identified age pathway, which is controlled by microRNA156 (miR156) and its target SQUAMOSA PROMOTER BINDING-LIKE (SPL) transcription factors, ensures plants flower under non-inductive conditions. In this review, I summarize the recent advance in understanding of the age pathway, focusing on the regulatory basis of the developmental decline in miR156 level by age and the molecular mechanism by which the age pathway is integrated into other flowering time pathways.

The growth-defense pivot: crisis management in plants mediated by LRR-RK surface receptors

Plants must adapt to their environment and require mechanisms for sensing their surroundings and responding appropriately. An expanded family of more than 200 leucine-rich repeat (LRR) receptor kinases (LRR-RKs) transduces fluctuating and often contradictory signals from the environment into changes in nuclear gene expression. Two LRR-RKs, BRASSINOSTEROID INSENSITIVE 1 (BRI1), a steroid receptor, and FLAGELLIN SENSITIVE 2 (FLS2), an innate immune receptor that recognizes bacterial flagellin, act cooperatively to partition necessary growth-defense trade-offs. BRI1 and FLS2 share common signaling components and slightly different activation mechanisms. BRI1 and FLS2 are paradigms for understanding the signaling mechanisms of LRR-containing receptors in plants.

Post-transcriptional regulation in root development

Plants constantly adapt their root system to the changing environmental conditions. This developmental plasticity is underpinned by changes in the profile of the mRNA expressed. Here we review how post-transcriptional modulation of gene expression control root development and growth. In particular we focus on the role of small RNA-mediated post-transcriptional regulation processes. Small RNAs play an important role in fine tuning gene expression during root formation and patterning, development of lateral organs and symbiosis, nutrient homeostasis, and other stress-related responses. We also highlight the impact of alternative splicing on root development and the establishment of symbiotic structures as well as the emerging role of long noncoding RNAs in root physiology.

Memory of the vernalized state in plants including the model grass Brachypodium distachyon

Plant species that have a vernalization requirement exhibit variation in the ability to "remember" winter - i.e., variation in the stability of the vernalized state. Studies in Arabidopsis have demonstrated that molecular memory involves changes in the chromatin state and expression of the flowering repressor FLOWERING LOCUS C, and have revealed that single-gene differences can have large effects on the stability of the vernalized state. In the perennial Arabidopsis relative Arabis alpina, the lack of memory of winter is critical for its perennial life history. Our studies of flowering behavior in the model grass Brachypodium distachyon reveal extensive variation in the vernalization requirement, and studies of a particular Brachypodium accession that has a qualitative requirement for both cold exposure and inductive day length to flower reveal that Brachypodium can exhibit a highly stable vernalized state.

Advances in genome studies in plants and animals

The area of plant and animal genomics covers the entire suite of issues in biology because it aims to determine the structure and function of genetic material. Although specific issues define research advances at an organism level, it is evident that many of the fundamental features of genome structure and the translation of encoded information to function share common ground. The Plant and Animal Genome (PAG) conference held in San Diego (California), in January each year provides an overview across all organisms at the genome level, and often it is evident that investments in the human area provide leadership, applications, and discoveries for researchers studying other organisms. This mini-review utilizes the plenary lectures as a basis for summarizing the trends in the genome-level studies of organisms, and the lectures include presentations by Ewan Birney (EBI, UK), Eric Green (NIH, USA), John Butler (NIST, USA), Elaine Mardis (Washington, USA), Caroline Dean (John Innes Centre, UK), Trudy Mackay (NC State University, USA), Sue Wessler (UC Riverside, USA), and Patrick Wincker (Genoscope, France). The work reviewed is based on published papers. Where unpublished information is cited, permission to include the information in this manuscript was obtained from the presenters.

Plant chromatin warms up in Madrid: meeting summary of the 3rd European Workshop on Plant Chromatin 2013, Madrid, Spain

The 3rd European Workshop on Plant Chromatin (EWPC) was held on August 2013 in Madrid, Spain. A number of different topics on plant chromatin were presented during the meeting, including new factors mediating Polycomb Group protein function in plants, chromatin-mediated reprogramming in plant developmental transitions, the role of histone variants, and newly identified chromatin remodeling factors. The function of interactions between chromatin and transcription factors in the modulation of gene expression, the role of chromatin dynamics in the control of nuclear processes and the influence of environmental factors on chromatin organization were also reported. In this report, we highlight some of the new insights emerging in this growing area of research, presented at the 3rd EWPC.

Footprints of the sun: memory of UV and light stress in plants

Sunlight provides the necessary energy for plant growth via photosynthesis but high light and particular its integral ultraviolet (UV) part causes stress potentially leading to serious damage to DNA, proteins, and other cellular components. Plants show adaptation to environmental stresses, sometimes referred to as "plant memory." There is growing evidence that plants memorize exposure to biotic or abiotic stresses through epigenetic mechanisms at the cellular level. UV target genes such as CHALCONE SYNTHASE (CHS) respond immediately to UV treatment and studies of the recently identified UV-B receptor UV RESISTANCE LOCUS 8 (UVR8) confirm the expedite nature of UV signaling. Considering these findings, an UV memory seems redundant. However, several lines of evidence suggest that plants may develop an epigenetic memory of UV and light stress, but in comparison to other abiotic stresses there has been relatively little investigation. Here we summarize the state of knowledge about acclimation and adaptation of plants to UV light and discuss the possibility of chromatin based epigenetic memory.

Epigenetic responses to heat stress at different time scales and the involvement of small RNAs

The hypothesis that plants can benefit from a memory of past stress exposure has recently attracted a lot of attention. Here, we discuss two different examples of heat stress memory to elucidate the potential benefits that epigenetic responses may provide at both the level of acclimation of the individual plant and adaptation at a species-wide level. Specifically, we discuss how microRNAs regulate the heat stress memory and thereby increase survival upon a recurring heat stress. Secondly, we review how a prolonged heat stress in a small interfering RNA-deficient background induces retrotransposition that is transmitted to the next generation, thus creating genetic variation for natural selection to act on. Collectively, these studies reveal a crucial role of short RNAs in heat stress memory across different time scales.

A chromatin modifying enzyme, SDG8, is involved in morphological, gene expression, and epigenetic responses to mechanical stimulation

Thigmomorphogenesis is viewed as being a response process of acclimation to short repetitive bursts of mechanical stimulation or touch. The underlying molecular mechanisms that coordinate changes in how touch signals lead to long-term morphological changes are enigmatic. Touch responsive gene expression is rapid and transient, and no transcription factor or DNA regulatory motif has been reported that could confer a genome wide mechanical stimulus. We report here on a chromatin modifying enzyme, SDG8/ASHH2, which can regulate the expression of many touch responsive genes identified in Arabidopsis. SDG8 is required for the permissive expression of touch induced genes; and the loss of function of sdg8 perturbs the maximum levels of induction on selected touch gene targets. SDG8 is required to maintain permissive H3K4 trimethylation marks surrounding the Arabidopsis touch-inducible gene TOUCH 3 (TCH3), which encodes a calmodulin-like protein (CML12). The gene neighboring was also slightly down regulated, revealing a new target for SDG8 mediated chromatin modification. Finally, sdg8 mutants show perturbed morphological response to wind-agitated mechanical stimuli, implicating an epigenetic memory-forming process in the acclimation response of thigmomorphogenesis.