Whole-cell cross-linking coupled to mass spectrometry is one of the few tools that can probe protein-protein interactions in intact cells. A very attractive reagent for this purpose is formaldehyde, ...a small molecule which is known to rapidly penetrate into all cellular compartments and to preserve the protein structure. In light of these benefits, it is surprising that identification of formaldehyde cross-links by mass spectrometry has so far been unsuccessful. Here we report mass spectrometry data that reveal formaldehyde cross-links to be the dimerization product of two formaldehyde-induced amino acid modifications. By integrating the revised mechanism into a customized search algorithm, we identify hundreds of cross-links from in situ formaldehyde fixation of human cells. Interestingly, many of the cross-links could not be mapped onto known atomic structures, and thus provide new structural insights. These findings enhance the use of formaldehyde cross-linking and mass spectrometry for structural studies.
The global shortage of fresh water is one of our most severe agricultural problems, leading to dry and saline lands that reduce plant growth and crop yield. Here we review recent work highlighting ...the molecular mechanisms allowing some plant species and genotypes to maintain productivity under water stress conditions, and suggest molecular modifications to equip plants for greater production in water‐limited environments. Aquaporins (AQPs) are thought to be the main transporters of water, small and uncharged solutes, and CO2 through plant cell membranes, thus linking leaf CO2 uptake from the intercellular airspaces to the chloroplast with water loss pathways. AQPs appear to play a role in regulating dynamic changes of root, stem and leaf hydraulic conductivity, especially in response to environmental changes, opening the door to using AQP expression to regulate plant water‐use efficiency. We highlight the role of vascular AQPs in regulating leaf hydraulic conductivity and raise questions regarding their role (as well as tonoplast AQPs) in determining the plant isohydric threshold, growth rate, fruit yield production and harvest index. The tissue‐ or cell‐specific expression of AQPs is discussed as a tool to increase yield relative to control plants under both normal and water‐stressed conditions.
Here we review the role of vascular, mesophyll and tonoplast AQPs in regulating the plant isohydric threshold. The tissue specific and cell specific activity of AQPs in controlling the membrane water and/or CO2 permeability is discussed as a tool to increase yield under both normal and water‐stressed conditions.
Different combinations of histone modifications have been proposed to signal distinct gene regulatory functions, but this area is poorly addressed by existing technologies. We applied high-throughput ...single-molecule imaging to decode combinatorial modifications on millions of individual nucleosomes from pluripotent stem cells and lineage-committed cells. We identified definitively bivalent nucleosomes with concomitant repressive and activating marks, as well as other combinatorial modification states whose prevalence varies with developmental potency. We showed that genetic and chemical perturbations of chromatin enzymes preferentially affect nucleosomes harboring specific modification states. Last, we combined this proteomic platform with single-molecule DNA sequencing technology to simultaneously determine the modification states and genomic positions of individual nucleosomes. This single-molecule technology has the potential to address fundamental questions in chromatin biology and epigenetic regulation.
BACKGROUND AND AIMS: Global climate models predict decreases in leaf stomatal conductance and transpiration due to increases in atmospheric CO₂. The consequences of these reductions are increases in ...soil moisture availability and continental scale run-off at decadal time-scales. Thus, a theory explaining the differential sensitivity of stomata to changing atmospheric CO₂ and other environmental conditions must be identified. Here, these responses are investigated using optimality theory applied to stomatal conductance. METHODS: An analytical model for stomatal conductance is proposed based on: (a) Fickian mass transfer of CO₂ and H₂O through stomata; (b) a biochemical photosynthesis model that relates intercellular CO₂ to net photosynthesis; and (c) a stomatal model based on optimization for maximizing carbon gains when water losses represent a cost. Comparisons between the optimization-based model and empirical relationships widely used in climate models were made using an extensive gas exchange dataset collected in a maturing pine (Pinus taeda) forest under ambient and enriched atmospheric CO₂. KEY RESULTS AND CONCLUSION: In this interpretation, it is proposed that an individual leaf optimally and autonomously regulates stomatal opening on short-term (approx. 10-min time-scale) rather than on daily or longer time-scales. The derived equations are analytical with explicit expressions for conductance, photosynthesis and intercellular CO₂, thereby making the approach useful for climate models. Using a gas exchange dataset collected in a pine forest, it is shown that (a) the cost of unit water loss λ (a measure of marginal water-use efficiency) increases with atmospheric CO₂; (b) the new formulation correctly predicts the condition under which CO₂-enriched atmosphere will cause increasing assimilation and decreasing stomatal conductance.
Since the emergence of next-generation sequencing (NGS) technologies, great effort has been put into the development of tools for analysis of the short reads. In parallel, knowledge is increasing ...regarding biases inherent in these technologies. Here we discuss four different biases we encountered while analyzing various Illumina datasets. These biases are due to both biological and statistical effects that in particular affect comparisons between different genomic regions. Specifically, we encountered biases pertaining to the distributions of nucleotides across sequencing cycles, to mappability, to contamination of pre-mRNA with mRNA, and to non-uniform hydrolysis of RNA. Most of these biases are not specific to one analyzed dataset, but are present across a variety of datasets and within a variety of genomic contexts. Importantly, some of these biases correlated in a highly significant manner with biological features, including transcript length, gene expression levels, conservation levels, and exon-intron architecture, misleadingly increasing the credibility of results due to them. We also demonstrate the relevance of these biases in the context of analyzing an NGS dataset mapping transcriptionally engaged RNA polymerase II (RNAPII) in the context of exon-intron architecture, and show that elimination of these biases is crucial for avoiding erroneous interpretation of the data. Collectively, our results highlight several important pitfalls, challenges and approaches in the analysis of NGS reads.
To predict how forests will respond to rising temperatures and atmospheric CO₂concentrations, we need to understand how trees respond to both of these environmental factors. In this review, we ...discuss the importance of scaling, moving from leaf‐level responses to those of the canopy, and from short‐term to long‐term responses of vegetation to climate change. While our knowledge of leaf‐level, instantaneous responses of photosynthesis, respiration, stomatal conductance, transpiration and water‐use efficiency to elevated CO₂and temperature is quite good, our ability to scale these responses up to larger spatial and temporal scales is less developed. We highlight which physiological processes are least understood at various levels of study, and discuss how ignoring differences in the spatial or temporal scale of a physiological process impedes our ability to predict how forest carbon and water fluxes forests will be altered in the future. We also synthesize data from the literature to show that light respiration follows a generalized temperature response across studies, and that the light compensation point of photosynthesis is reduced by elevated growth CO₂. Lastly, we emphasize the need to move beyond single factorial experiments whenever possible, and to combine both CO₂and temperature treatments in studies of tree performance.
The role of evapotranspiration (ET) in the global, continental, regional, and local water cycles is reviewed. Elevated atmospheric CO2, air temperature, vapor pressure deficit (D), turbulent ...transport, radiative transfer, and reduced soil moisture all impact biotic and abiotic processes controlling ET that must be extrapolated to large scales. Suggesting a blueprint to achieve this link is the main compass of this review. Leaf‐scale transpiration (fe) as governed by the plant biochemical demand for CO2 is first considered. When this biochemical demand is combined with mass transfer formulations, the problem remains mathematically intractable, requiring additional assumptions. A mathematical “closure” that assumes stomatal aperture is autonomously regulated so as to maximize the leaf carbon gain while minimizing water loss is proposed, which leads to analytical expressions for leaf‐scale transpiration. This formulation predicts well the effects of elevated atmospheric CO2 and increases in D on fe. The case of soil moisture stress is then considered using extensive gas exchange measurements collected in drought studies. Upscaling the fe to the canopy is then discussed at multiple time scales. The impact of limited soil water availability within the rooting zone on the upscaled ET as well as some plant strategies to cope with prolonged soil moisture stress are briefly presented. Moving further up in direction and scale, the soil‐plant system is then embedded within the atmospheric boundary layer, where the influence of soil moisture on rainfall is outlined. The review concludes by discussing outstanding challenges and how to tackle them by means of novel theoretical, numerical, and experimental approaches.
Key Points
Effects of elevated CO2 and warming on ET evaluated
ET scaling from leaf to globe reviewed
Global‐ and leaf‐level ET most constrained
In mammals, cellular identity is defined through strict regulation of chromatin modifications and DNA methylation that control gene expression. Methylation of cytosines at CpG sites in the genome is ...mainly associated with suppression; however, the reason for enhancer-specific methylation is not fully understood. We used sequential ChIP-bisulfite-sequencing for H3K4me1 and H3K27ac histone marks. By collecting data from the same genomic region, we identified enhancers differentially methylated between these two marks. We observed a global gain of CpG methylation primarily in H3K4me1-marked nucleosomes during mouse embryonic stem cell differentiation. This gain occurred largely in enhancer regions that regulate genes critical for differentiation. The higher levels of DNA methylation in H3K4me1- versus H3K27ac-marked enhancers, despite it being the same genomic region, indicates cellular heterogeneity of enhancer states. Analysis of single-cell RNA-seq profiles demonstrated that this heterogeneity correlates with gene expression during differentiation. Furthermore, heterogeneity of enhancer methylation correlates with transcription start site methylation. Our results provide insights into enhancer-based functional variation in complex biological systems.
Mammalian gene regulation is dependent on tissue-specific enhancers that can act across large distances to influence transcriptional activity. Mapping experiments have identified hundreds of ...thousands of putative enhancers whose functionality is supported by cell type-specific chromatin signatures and striking enrichments for disease-associated sequence variants. However, these studies did not address the in vivo functions of the putative elements or their chromatin states and did not determine which genes, if any, a given enhancer regulates. Here we present a strategy to investigate endogenous regulatory elements by selectively altering their chromatin state using programmable reagents. Transcription activator-like (TAL) effector repeat domains fused to the LSD1 histone demethylase efficiently remove enhancer-associated chromatin modifications from target loci, without affecting control regions. We find that inactivation of enhancer chromatin by these fusion proteins frequently causes downregulation of proximal genes, revealing enhancer target genes. Our study demonstrates the potential of epigenome editing tools to characterize an important class of functional genomic elements.
During meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex ...chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.
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