Philip Wigge

University of Cambridge | Cam · Sainsbury Laboratory

Heat stress significantly affects global agricultural yield and food security and as climate change is expected to increase the frequency and severity of heatwaves, this is a growing challenge. Tomato plants are prone to heat stress exposure both in the field and in greenhouses, making heat stress resilience a key trait for breeding. While the iden...

Phase separation is an important mechanism for regulating various cellular functions. The EARLY FLOWERING 3 (ELF3) protein, an essential element of the EVENING COMPLEX (EC) involved in circadian clock regulation, has been shown to undergo phase separation. ELF3 is known to significantly influence elongation growth and flowering time regulation, and...

Electrophoretic mobility shift assays (EMSAs) of DNA-binding proteins and labeled DNA allow the qualitative and quantitative characterization of protein-DNA complex formation using native (nondenaturing) polyacrylamide or agarose gel electrophoresis. By varying the incubation temperature of the protein-DNA binding reaction and maintaining this temp...

RNA molecules play crucial roles in gene expression regulation and cellular signaling, and these functions are governed by the formation of RNA secondary and tertiary structures. These structures are highly dynamic and subject to rapid changes in response to environmental cues, temperature in particular. Thermosensitive RNA secondary structures hav...

Background Daylength is a key seasonal cue for animals and plants. In cereals, photoperiodic responses are a major adaptive trait, and alleles of clock genes such as PHOTOPERIOD1 (PPD1) and EARLY FLOWERING3 (ELF3) have been selected for in adapting barley and wheat to northern latitudes. How monocot plants sense photoperiod and integrate this infor...

In 1998, Bill Gray and colleagues showed that warm temperatures trigger arabidopsis hypocotyl elongation in an auxin-dependent manner. This laid the foundation for a vibrant research discipline. With several active members of the 'thermomorphogenesis' community, we here reflect on 25 years of elevated ambient temperature research and look to the fu...

Liquid-liquid phase separation (LLPS) is an important mechanism enabling the dynamic compartmentalization of macromolecules, including complex polymers such as proteins and nucleic acids, and occurs as a function of the physicochemical environment. In the model plant, Arabidopsis thaliana, LLPS by the protein EARLY FLOWERING3 (ELF3) occurs in a tem...

Plants show remarkable phenotypic plasticity and are able to adjust their morphology and development to diverse environmental stimuli. Morphological acclimation responses to elevated ambient temperatures are collectively termed thermomorphogenesis. In Arabidopsis thaliana, morphological changes are coordinated to a large extent by the transcription...

Plants use photoperiodism to activate flowering in response to a particular daylength. In rice, flowering is accelerated in short-day conditions, and even a brief exposure to light during the dark period (night-break) is sufficient to delay flowering. Although many of the genes involved in controlling flowering in rice have been uncovered, how the...

Many plants are able to regenerate upon cutting, and this process can be enhanced in vitro by incubating explants on hormone-supplemented media. While such protocols have been used for decades, little is known about the molecular details of how incubation conditions influence their efficiency. In this study, we find that warm temperature promotes b...

Molecular mechanisms of how constant temperatures affect flowering time have been largely characterized in the model plant Arabidopsis thaliana; however, the effect of natural daily variable temperature outside laboratories is only partly explored. Several flowering genes have been shown to play important roles in temperature responses, including P...

Light perception at dawn plays a key role in coordinating multiple molecular processes and in entraining the plant circadian clock. An Arabidopsis mutant lacking the main photoreceptors however still shows clock entrainment, indicating that the integration of light into the morning transcriptome is not well understood. We performed a high-resolutio...

The correct name of the 3rd Author is presented in this paper.

Initiation of flowering is a crucial developmental event that requires both internal and environmental signals to determine when floral transition should occur to maximize reproductive success. Ambient temperature is one of the key environmental signals that highly influence flowering time, not only seasonally but also in the context of drastic tem...

In temperate trees, optimal timing and quality of flowering directly depend on adequate winter dormancy progression, regulated by a combination of chilling and warm temperatures. Physiological, genetic and functional genomic studies have shown that hormones play a key role in bud dormancy establishment, maintenance and release. We combined physiolo...

Temperature controls plant growth and development, and climate change has already altered the phenology of wild plants and crops¹. However, the mechanisms by which plants sense temperature are not well understood. The evening complex is a major signalling hub and a core component of the plant circadian clock2,3. The evening complex acts as a temper...

This book on the physiology of vegetable crops focuses on the activities and functions of vegetables, defined as herbaceous plants that are harvested for edible parts that can be consumed fresh or with little preparation. Physiology deals with the growth and development processes of these plants, and while this book is focused primarily on the orga...

Temperature is a major environmental cue affecting plant growth and development. Plants often experience higher temperatures in the context of a 24 h day–night cycle, with temperatures peaking in the middle of the day. Here, we find that the transcript encoding the bHLH transcription factor PIF7 undergoes a direct increase in translation in respons...

The Evening Complex (EC), composed of the DNA binding protein LUX ARRHYTHMO (LUX) and two additional proteins EARLY FLOWERING 3 (ELF3) and ELF4, is a transcriptional repressor complex and a core component of the plant circadian clock. In addition to maintaining oscillations in clock gene expression, the EC also participates in temperature and light...

Upon detecting abiotic or biotic stress, plants generally reduce their growth, enabling resources to be conserved and diverted to stress response mechanisms. In Arabidopsis thaliana, the AT-hook motif nuclear-localized (AHL) transcription factor family has been implicated in restricting rosette growth in response to stress. However, the mechanism b...

Chromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors and DNA. This technique in combination with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq prot...

Background: Bud dormancy is a crucial stage in perennial trees and allows survival over winter to ensure optimal flowering and fruit production. Recent work highlighted physiological and molecular events occurring during bud dormancy in trees. However, they usually examined bud development or bud dormancy in isolation. In this work, we aimed to fu...

The Evening Complex (EC) is a core component of the Arabidopsis (Arabidopsis thaliana) circadian clock, which represses target gene expression at the end of the day and integrates temperature information to coordinate environmental and endogenous signals. Here we show that the EC induces repressive chromatin structure to regulate the evening transc...

Background Bud dormancy is a crucial stage in perennial trees and allows survival over winter to ensure optimal flowering and fruit production. Recent work highlighted physiological and molecular events occurring during bud dormancy in trees. However, they usually examined bud development or bud dormancy in isolation. In this work, we aimed to furt...

Day length is a key indicator of seasonal information that determines major patterns of behavior in plants and animals. Photoperiodism has been described in plants for about 100 years, but the underlying molecular mechanisms of day length perception and signal transduction in many systems are not well understood. In trees, photoperiod perception pl...

The Evening Complex (EC), composed of the DNA-binding protein LUX ARRHYTHMO (LUX) and two additional proteins, EARLY FLOWERING 3 (ELF3) and ELF4, is a transcriptional repressor complex and a core component of the plant circadian clock. In addition to maintaining oscillations in clock gene expression, the EC also participates in temperature and ligh...

In temperate trees, optimal timing and quality of flowering directly depend on adequate winter dormancy progression, regulated by a combination of chilling and warm temperatures. Physiological, genetic and functional genomic studies have shown that hormones play a key role in bud dormancy establishment, maintenance and release. We combined physiolo...

Chromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors, and DNA. This technique combined with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq protocol...

Environmental factors shape the phenotypes of multicellular organisms. The production of stomata-the epidermal pores required for gas exchange in plants-is highly plastic and provides a powerful platform to address environmental influence on cell differentiation [1-3]. Rising temperatures are already impacting plant growth, a trend expected to wors...

Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) is a powerful technique to investigate in vivo transcription factor (TF) binding to DNA, as well as chromatin marks. Here we provide a detailed protocol for all the key steps to perform ChIP-seq in Arabidopsis thaliana roots, also working on other A. thaliana tissues...

Two Gene Ontology (GO) enrichment tools, GOrilla and AgriGO, were used for enrichment analysis and all genes that passed the filters used when calculating Z-scores were used as background. The top five most enriched GO terms from each analysis are shown.

Promoter motif enrichment was performed using HOMER2. Sequences 1 kb upstream of the TSS were obtained from TAIR and these were used to search for known motifs. Sequences 1 kb upstream of all genes that passed the filters used when calculating Z-scores were used as background sequences. The top five most enriched motifs are shown.

Table S4. List of Genes Found in the Clusters Described in This Study, Related to Figures 1, 3, and 4

Temperature is a key environmental variable influencing plant growth and survival. Protection against high temperature stress in eukaryotes is coordinated by heat shock factors (HSFs), transcription factors that activate the expression of protective chaperones such as HEAT SHOCK PROTEIN 70 (HSP70); however, the pathway by which temperature is sense...

Plants have significantly more transcription factor (TF) families than animals and fungi, and plant TF families tend to contain more genes-these expansions are linked to adaptation to environmental stressors (Shiu et al., 2005; Charoensawan et al., 2010). Many TF family members bind to similar or identical sequence motifs, such as G-boxes (CACGTG),...

Temperature influences the distribution, range and phenology of plants. The key transcriptional activators of the heat shock response in eukaryotes, the heat shock factors (HSFs), have undergone a large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in ambient temperature changes is less well underst...

Plants maximize their fitness by adjusting their growth and development in response to signals such as light and temperature. The circadian clock provides a mechanism for plants to anticipate events such as sunrise and adjust their transcriptional programmes. However, the underlying mechanisms by which plants coordinate environmental signals with e...

Transcript levels are a critical determinant of the proteome and hence cellular function. Because the transcriptome is an outcome of the interactions between genes and their products, it may be accurately represented by a subset of transcript abundances. We develop a method, Tradict (transcriptome predict), capable of learning and using the express...

GO-Term size analysis: M. musculus

Test-set PCC for the bottom 20 and top 20 A. thaliana programs when gene-to-program assignments are 100% random.

Selected globally representative markers for A. thaliana

Selected globally representative markers for M. musculus

M. musculus transcriptional programs, their prospective prediction accuracy, and other properties

Number of SRA RNA-Seq records for several model organisms (current as of September 23, 2016)

Supplementary Figures, Supplementary Notes and Supplementary References

GO-Term size analysis: A. thaliana

A. thaliana transcriptional programs, their prospective prediction accuracy, and other properties

Plants have significantly more transcription factor (TF) families than animals and fungi, and plant TF families tend to contain more genes—these expansions are linked to adaptation to environmental stressors (1, 2). Many TF family members bind to similar or identical sequence motifs, such as G-boxes (CACGTG), so it is difficult to predict regulator...

Plants use context-dependent information to calibrate growth responses to temperature signals. A new study shows that plants modulate their sensitivity to temperature depending on whether or not they are in direct sunlight. This enables them to make adaptive decisions in a complex natural environment.

Combining heat and light responses Plants integrate a variety of environmental signals to regulate growth patterns. Legris et al. and Jung et al. analyzed how the quality of light is interpreted through ambient temperature to regulate transcription and growth (see the Perspective by Halliday and Davis). The phytochromes responsible for reading the...

Combining heat and light responses Plants integrate a variety of environmental signals to regulate growth patterns. Legris et al. and Jung et al. analyzed how the quality of light is interpreted through ambient temperature to regulate transcription and growth (see the Perspective by Halliday and Davis). The phytochromes responsible for reading the...

Transcript levels are a critical determinant of the proteome and hence cellular function. Because the transcriptome is an outcome of the interactions between genes and their products, it may be accurately represented by a subset of transcript abundances. We developed a method, Tradict ( tra nscriptome pre dict ), capable of learning and using the e...

Temperature is a major factor governing the distribution and seasonal behaviour of plants. Being sessile, plants are highly responsive to small differences in temperature and adjust their growth and development accordingly. The suite of morphological and architectural changes induced by high ambient temperatures, below the heat-stress range, is col...

A key challenge for understanding transcriptional regulation is being able to measure transcription factor (TF)-DNA binding events with sufficient spatial and temporal resolution; that is, when and where TFs occupy their cognate sites. A recent study by Para et al. has highlighted the dynamics underlying the activation of gene expression by a maste...

Plant development is highly responsive to ambient temperature, and this trait has been linked to the ability of plants to adapt to climate change [1 • Fitter A.H. • Fitter R.S. Rapid changes in flowering time in British plants.Science. 2002; 296: 1689-1691 • Crossref • PubMed • Scopus (949) • Google Scholar ]. The mechanisms by which natural popu...

Temperature is a major determinant of plant growth, development and success. Understanding how plants respond to temperature is particularly relevant in a warming climate. Plant immune responses are often suppressed above species-specific critical temperatures. This is also true for intraspecific hybrids of Arabidopsis thaliana that express hybrid...

Plants are exposed to daily and seasonal fluctuations in temperature. Within the 'ambient' temperature range (about 12-27°C for Arabidopsis) temperature differences have large effects on plant growth and development, disease resistance pathways and the circadian clock without activating temperature stress pathways. It is this developmental sensing...

The floral transition is a key decision during plant development. While different species have evolved diverse pathways to respond to different environmental cues to flower in the correct season, key properties such as irreversibility and robustness to fluctuating signals appear to be conserved. We have used mathematical modeling to demonstrate how...

Crop plants are highly sensitive to ambient temperature, with a 1 oC difference in temperature sufficient to affect development and yield. Monocot crop plants are particularly vulnerable to higher temperatures during the reproductive and grain-filling phases. The molecular mechanisms by which temperature influences grain development are however unk...

During flowering, primordia on the flanks of the shoot apical meristem are specified to form flowers instead of leaves. Like many plants, Arabidopsis thaliana integrates environmental and endogenous signals to control the timing of reproduction. To study the underlying regulatory logic of the floral transition, we used a combination of modeling and...

Comment on: Charoensawan V, et al. Mol Cell 2012; 47:183-92.

Plant growth and development are strongly affected by small differences in temperature. Current climate change has already altered global plant phenology and distribution, and projected increases in temperature pose a significant challenge to agriculture. Despite the important role of temperature on plant development, the underlying pathways are un...

At high ambient temperature, plants display dramatic stem elongation in an adaptive response to heat. This response is mediated by elevated levels of the phytohormone auxin and requires auxin biosynthesis, signaling, and transport pathways. The mechanisms by which higher temperature results in greater auxin accumulation are unknown, however. A basi...

A recent flurry of activity has defined the protein FLOWERING LOCUS T (FT) as a mobile signal or 'florigen' that induces flowering. A new study has shown that a 14-3-3 protein links FT to a transcription factor at the plant apex to initiate flowering.

Plants synchronise their flowering with the seasons to maximise reproductive fitness. While plants sense environmental conditions largely through the leaves, the developmental decision to flower occurs in the shoot apex, requiring the transmission of flowering information, sometimes over quite long distances. Interestingly, despite the enormous div...

The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Toda...

Plants are highly sensitive to temperature and can perceive a difference of as little as 1 degrees C. How temperature is sensed and integrated in development is unknown. In a forward genetic screen in Arabidopsis, we have found that nucleosomes containing the alternative histone H2A.Z are essential to perceiving ambient temperature correctly. Genot...

Flexible adaptation to environmental changes is essential for plants. Recent studies suggest that a group of basic helix-loop-helix transcription factors play a central role in the crosstalk between environmental cues and hormone signalling.

A new study provides insight into the way plants integrate information from the environment to anticipate the onset of winter. Plants are able to combine information about light quality and ambient temperature to activate the cold- acclimation pathway.

Plants are sessile organisms and must respond to changes in environmental conditions. Flowering time is a key developmental switch that is affected by both day length and temperature. Environmental cues are sensed by the leaves while the responses occur at the apex, requiring long-range communication within the plant. For many years it has been kno...

INTRODUCTION Because transformation of Arabidopsis is a relatively long-winded process, it is a good idea to verify the presence of the T-DNA plasmid in the Agrobacterium strain before proceeding with transformation experiments. This protocol describes a method to determine the presence of plasmid DNA in an Agrobacterium culture. Compared to select...

The transition to flowering is one of the most important developmental decisions made by plants. Classical studies have highlighted the importance of photoperiod in controlling flowering time. More recently, the identification of mutants specifically affected in the photoperiod pathway in the model system Arabidopsis thaliana has enabled the flower...

Since plants are sessile they must be able to sense and rapidly respond to changes in ambient temperature. Key aspects of plant development, including the transition to flowering and the circadian clock, have important inputs from ambient temperature. In the model system Arabidopsis thaliana, molecular candidates for mediating these roles have rece...

Flowering of Arabidopsis is regulated by several environmental and endogenous signals. An important integrator of these inputs is the FLOWERING LOCUS T (FT) gene, which encodes a small, possibly mobile protein. A primary response to floral induction is the activation of FT RNA expression in leaves. Because flowers form at a distant site, the shoot...

A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Plant Biology.

A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Plant Biology.