S. Vinod Kumar

H2A.Z-Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis

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. Genotypes deficient in incorporating H2A.Z into nucleosomes phenocopy warm grown plants, and show a striking constitutive warm temperature transcriptome. We show that nucleosomes containing H2A.Z display distinct responses to temperature in vivo, independently of transcription. Using purified nucleosomes, we are able to show that H2A.Z confers distinct DNA-unwrapping properties on nucleosomes, indicating a direct mechanism for the perception of temperature through DNA-nucleosome fluctuations. Our results show that H2A.Z-containing nucleosomes provide thermosensory information that is used to coordinate the ambient temperature transcriptome. We observe the same effect in budding yeast, indicating that this is an evolutionarily conserved mechanism.

Transcription factor PIF4 controls the thermosensory activation of flowering

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 unknown. It has previously been shown that thermal acceleration of flowering is dependent on the florigen, FLOWERING LOCUS T (FT). How this occurs is, however, not understood, because the major pathway known to upregulate FT, the photoperiod pathway, is not required for thermal acceleration of flowering. Here we demonstrate a direct mechanism by which increasing temperature causes the bHLH transcription factor PHYTOCHROME INTERACTING FACTOR4 (PIF4) to activate FT. Our findings provide a new understanding of how plants control their timing of reproduction in response to temperature. Flowering time is an important trait in crops as well as affecting the life cycles of pollinator species. A molecular understanding of how temperature affects flowering will be important for mitigating the effects of climate change.

PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) regulates auxin biosynthesis at high temperature

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 basic helix-loop-helix transcription factor, PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), is also required for hypocotyl elongation in response to high temperature. PIF4 also acts redundantly with its homolog, PIF5, to regulate diurnal growth rhythms and elongation responses to the threat of vegetative shade. PIF4 activity is reportedly limited in part by binding to both the basic helix-loop-helix protein LONG HYPOCOTYL IN FAR RED 1 and the DELLA family of growth-repressing proteins. Despite the importance of PIF4 in integrating multiple environmental signals, the mechanisms by which PIF4 controls growth are unknown. Here we demonstrate that PIF4 regulates levels of auxin and the expression of key auxin biosynthesis genes at high temperature. We also identify a family of SMALL AUXIN UP RNA (SAUR) genes that are expressed at high temperature in a PIF4-dependent manner and promote elongation growth. Taken together, our results demonstrate direct molecular links among PIF4, auxin, and elongation growth at high temperature.

DET1 and HY5 Control PIF4-Mediated Thermosensory Elongation Growth through Distinct Mechanisms

Summary Plant growth and development are defined by environmental cues. The transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is the central signaling hub that integrates environmental cues, including light and temperature, to regulate growth and development. The thermosensory mechanisms controlling the PIF4-mediated temperature response, and its integration with other environmental responses, remain poorly understood. DE-ETIOLATED 1 (DET1) and CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1), key regulators of light signaling, have been proposed to control thermosensory growth by transcriptional regulation of PIF4, through ELONGATED HYPOCOTYL 5 (HY5). Here, we show that DET1/COP1 and HY5 regulate thermosensory elongation through distinct mechanisms. DET1 and COP1 are essential for promoting PIF4 expression and stabilizing PIF4 protein. Furthermore, HY5 inhibits elongation growth through competitive chromatin binding to PIF4 targets, not through transcriptional regulation of PIF4. Our findings reveal a mechanistic framework in which DET1/COP1 and HY5 regulatory modules act independently to regulate growth through the environmental signal integrator PIF4.

Delineation of metabolic gene clusters in plant genomes by chromatin signatures

Plants are a tremendous source of diverse chemicals, including many natural product-derived drugs. It has recently become apparent that the genes for the biosynthesis of numerous different types of plant natural products are organized as metabolic gene clusters, thereby unveiling a highly unusual form of plant genome architecture and offering novel avenues for discovery and exploitation of plant specialized metabolism. Here we show that these clustered pathways are characterized by distinct chromatin signatures of histone 3 lysine trimethylation (H3K27me3) and histone 2 variant H2A.Z, associated with cluster repression and activation, respectively, and represent discrete windows of co-regulation in the genome. We further demonstrate that knowledge of these chromatin signatures along with chromatin mutants can be used to mine genomes for cluster discovery. The roles of H3K27me3 and H2A.Z in repression and activation of single genes in plants are well known. However, our discovery of highly localized operon-like co-regulated regions of chromatin modification is unprecedented in plants. Our findings raise intriguing parallels with groups of physically linked multi-gene complexes in animals and with clustered pathways for specialized metabolism in filamentous fungi.

PIF4 Coordinates Thermosensory Growth and Immunity in Arabidopsis

Summary Temperature is a key seasonal signal that shapes plant growth. Elevated ambient temperature accelerates growth and developmental transitions [1] while compromising plant defenses, leading to increased susceptibility [2, 3]. Suppression of immunity at elevated temperature is at the interface of trade-off between growth and defense [2, 4]. Climate change and the increase in average growth-season temperatures threaten biodiversity and food security [5, 6]. Despite its significance, the molecular mechanisms that link thermosensory growth and defense responses are not known. Here we show that PHYTOCHROME INTERACTING FACTOR 4 (PIF4)-mediated thermosensory growth and architecture adaptations are directly linked to suppression of immunity at elevated temperature. PIF4 positively regulates growth and development and negatively regulates immunity. We also show that natural variation of PIF4-mediated temperature response underlies variation in the balance between growth and defense among Arabidopsis natural strains. Importantly, we find that modulation of PIF4 function alters temperature sensitivity of defense. Perturbation of PIF4-mediated growth has resulted in temperature-resilient disease resistance. This study reveals a molecular link between thermosensory growth and immunity in plants. Elucidation of the molecular mechanisms that define environmental signal integration is key to the development of novel strategies for breeding temperature-resilient disease resistance in crops.

Temperature Modulates Tissue-Specification Program to Control Fruit Dehiscence in Brassicaceae

Plants respond to diurnal and seasonal changes in temperature by reprogramming vital developmental pathways. Understanding the molecular mechanisms that define environmental modulation of plant growth and reproduction is critical in the context of climate change that threatens crop yield worldwide. Here, we report that elevated temperature accelerates fruit dehiscence in members of the Brassicaceae family including the model plant Arabidopsis thaliana and important crop species. Arabidopsis fruit development is controlled by a network of interacting regulatory genes. Among them, the INDEHISCENT (IND) gene is a key regulator of the valve-margin tissue that mediates fruit opening, hence facilitating fruit dehiscence. We demonstrated that the valve-margin development is accelerated at higher temperature and that IND is targeted for thermosensory control. Our results reveal that IND upregulation is facilitated via temperature-induced chromatin dynamics leading to accelerated valve-margin specification and dispersal of the seed. Specifically, we show that temperature-induced changes in IND expression are associated with thermosensory H2A.Z nucleosome dynamics. These findings establish a molecular framework connecting tissue identity with thermal sensing and set out directions for the production of temperature-resilient crops.

Studying Transcription Factor Binding to Specific Genomic Loci by Chromatin Immunoprecipitation (ChIP).

Plant hormone signaling involves complex transcriptional networks, where transcription factors orchestrate the control of specific gene expression. These networks include cross talk between hormone signaling pathways, and the integration of environmental signals and the developmental program. Understanding how particular transcription factors respond and integrate specific signals is crucial in order to understand the basic mechanisms of hormonal signaling and cross talk. Studying transcription factor binding at specific genomic loci by chromatin immunoprecipitation (ChIP) is therefore a valuable technique in order to analyze transcriptional regulation. The method is based on cross-linking proteins to DNA, the isolation of chromatin, and immunoprecipitation of a transcription factor of interest. The attached DNA is then recovered and analyzed by quantitative real-time PCR in order to establish binding sites of the respective transcription factor. Here, we present a relatively simple and short protocol for ChIP on single loci.

Hot n' Cold: Molecular Signatures of Domestication Bring Fresh Insights into Environmental Adaptation.

Recent investigations of divergent rice genotypes have identified previously unknown molecular adaptations conferring heat and chilling tolerance in their corresponding local environments (Figure 1). These studies shed new light both on the domestication of rice and environmental adaptation strategies.

H2A.Z at the Core of Transcriptional Regulation in Plants

H2A.Z, an evolutionarily conserved variant form of canonical H2A, has been widely recognized to have decisive roles in multiple cellular processes through its influence on chromatin structure and dynamics in eukaryotes. Many of its effects on regulating chromatin function have been attributed to its role in modulating nucleosome dynamics and DNA methylation. In plants, H2A.Z plays critical roles in multiple processes, such as growth and development, phase transitions, and response to the environment. Despite the progress made in understanding its role in these processes, several aspects of H2A.Z biology, such as the specificity and regulation of its incorporation and action mechanism in transcriptional regulation, remained elusive. Nevertheless, recent discoveries in plants discussed here have provided the much-needed momentum in solving some of the mysteries associated with H2A.Z (Figure 1).