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An expanded registry of candidate cis -regulatory elements
Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, the ENCODE consortium mapped biochemical signals across hundreds of cell types and tissues and integrated these data to develop a registry containing 0.9 million human and 300,000 mouse candidate cis-regulatory elements (cCREs) annotated with potential functions. Here we have expanded the registry to include 2.37 million human and 967,000 mouse cCREs, leveraging new ENCODE datasets and enhanced computational methods. This expanded registry covers hundreds of unique cell and tissue types, providing a comprehensive understanding of gene regulation. Functional characterization data from assays such as STARR-seq, massively parallel reporter assay, CRISPR perturbation and transgenic mouse assays have profiled more than 90% of human cCREs, revealing complex regulatory functions. We identified thousands of novel silencer cCREs and demonstrated their dual enhancer and silencer roles in different cellular contexts. Integrating the registry with other ENCODE annotations facilitates genetic variation interpretation and trait-associated gene identification, exemplified by the identification of KLF1 as a novel causal gene for red blood cell traits. This expanded registry is a valuable resource for studying the regulatory genome and its impact on health and disease.
All the light we cannot see: Climate manipulations leave short and long‐term imprints in spectral reflectance of trees
Abstract Anthropogenic climate change, particularly changes in temperature and precipitation, affects plants in multiple ways. Because plants respond dynamically to stress and acclimate to changes in growing conditions, diagnosing quantitative plant‐environment relationships is a major challenge. One approach to this problem is to quantify leaf responses using spectral reflectance, which provides rapid, inexpensive, and nondestructive measurements that capture a wealth of information about genotype as well as phenotypic responses to the environment. However, it is unclear how warming and drought affect spectra. To address this gap, we used an open‐air field experiment that manipulates temperature and rainfall in 36 plots at two sites in the boreal‐temperate ecotone of northern Minnesota, USA. We collected leaf spectral reflectance (400–2400 nm) at the peak of the growing season for three consecutive years on juveniles (two to six years old) of five tree species planted within the experiment. We hypothesized that these mid‐season measurements of spectral reflectance capture a snapshot of the leaf phenotype encompassing a suite of physiological, structural, and biochemical responses to both long‐ and short‐time scale environmental conditions. We show that the imprint of environmental conditions experienced by plants hours to weeks before spectral measurements is linked to regions in the spectrum associated with stress, namely the water absorption regions of the near‐infrared and short‐wave infrared. In contrast, the environmental conditions plants experience during leaf development leave lasting imprints on the spectral profiles of leaves, attributable to leaf structure and chemistry (e.g., pigment content and associated ratios). Our analyses show that after accounting for baseline species spectral differences, spectral responses to the environment do not differ among the species. This suggests that building a general framework for understanding forest responses to climate change through spectral metrics may be possible, likely having broader implications if the common responses among species detected here represent a widespread phenomenon. Consequently, these results demonstrate that examining the entire spectrum of leaf reflectance for environmental imprints in contrast to single features (e.g., indices and traits) improves inferences about plant‐environment relationships, which is particularly important in times of unprecedented climate change.
Mesophyll conductance response to short-term changes in p CO 2 is related to leaf anatomy and biochemistry in diverse C 4 grasses
Mesophyll CO 2 conductance (g m ) in C 3 species responds to short-term (minutes) changes in environment potentially due to changes in leaf anatomical and biochemical properties and measurement artefacts. Compared with C 3 species, there is less information on g m responses to short-term changes in environmental conditions such as partial pressure of CO 2 (pCO 2 ) across diverse C 4 species and the potential determinants of these responses. Using 16 C 4 grasses we investigated the response of g m to short-term changes in pCO 2 and its relationship with leaf anatomy and biochemistry. In general, g m increased as pCO 2 decreased (statistically significant increase in 12 species), with percentage increases in gm ranging from +13% to +250%. Greater increase in g m at low pCO 2 was observed in species exhibiting relatively thinner mesophyll cell walls along with greater mesophyll surface area exposed to intercellular air spaces, leaf N, photosynthetic capacity and activities of phosphoenolpyruvate carboxylase and Rubisco. Species with greater CO 2 responses of g m were also able to maintain their leaf water-use efficiencies (TE i ) under low CO 2 . Our study advances understanding of CO 2 response of g m in diverse C 4 species, identifies the key leaf traits related to this response and has implications for improving C 4 photosynthetic models and TE i through modification of g m .
Bridging 20 Years of Soil Organic Matter Frameworks: Empirical Support, Model Representation, and Next Steps
Abstract In the past few decades, there has been an evolution in our understanding of soil organic matter (SOM) dynamics from one of inherent biochemical recalcitrance to one deriving from plant‐microbe‐mineral interactions. This shift in understanding has been driven, in part, by influential conceptual frameworks which put forth hypotheses about SOM dynamics. Here, we summarize several focal conceptual frameworks and derive from them six controls related to SOM formation, (de)stabilization, and loss. These include: (a) physical inaccessibility; (b) organo‐mineral and ‐metal stabilization; (c) biodegradability of plant inputs; (d) abiotic environmental factors; (e) biochemical reactivity and diversity; and (f) microbial physiology and morphology. We then review the empirical evidence for these controls, their model representation, and outstanding knowledge gaps. We find relatively strong empirical support and model representation of abiotic environmental factors but disparities between data and models for biochemical reactivity and diversity, organo‐mineral and ‐metal stabilization, and biodegradability of plant inputs, particularly with respect to SOM destabilization for the latter two controls. More empirical research on physical inaccessibility and microbial physiology and morphology is needed to deepen our understanding of these critical SOM controls and improve their model representation. The SOM controls are highly interactive and also present some inconsistencies which may be reconciled by considering methodological limitations or temporal and spatial variation. Future conceptual frameworks must simultaneously refine our understanding of these six SOM controls at various spatial and temporal scales and within a hierarchical structure, while incorporating emerging insights. This will advance our ability to accurately predict SOM dynamics.
Biochemical properties of glycerol kinase from the hypersaline-adapted archaeon Haloferax volcanii
ABSTRACT Extremophilic microorganisms are promising candidates for industrial and analytical biocatalysis.Haloferax volcanii, a halophilic archaeon that prefers glycerol over glucose, channels this substrate into central metabolism through glycerol kinase (GK). Here, we report the biochemical properties ofH. volcaniiGK and its potential for biotechnological applications. An N-terminal His-tagged GK was functionalin vivoand yielded 3 mg/L culture—4.5 times more enzyme than a C-terminal StrepII-tagged version. Size exclusion chromatography revealed a glycerol-induced oligomeric shift from homodimer to a dimer-dominant state with detectable tetramer. The purified enzyme showed robust activity across broad pH and salinity ranges, with optimal activity at 100 mM NaCl and 50°C–60°C. It retained catalytic activity in 5%–10% dimethyl sulfoxide (DMSO) and crude glycerol containing methanol. His-GK was freeze-thaw stable and thermotolerant in 2 M NaCl buffers. In the absence of ligands, the enzyme’s melting temperature (T m ) was 80°C. Glycerol increased the T m to 85°C, and combinations with MgCl₂ (84°C) or ATP (88°C) provided further stabilization. The highest T m (89°C) occurred with all three ligands, suggesting a cumulative stabilizing effect. Kinetic analyses revealed positive cooperativity for glycerol, ATP, and Mg² + ; Mn² + and Co² + also supported the activity.H. volcaniiGK is the first known GK to exhibit positive cooperativity with glycerol and ATP. Its high stability and substrate flexibility support its use in biodiesel waste valorization,in vitrobiocatalysis, and biosensor development—applications demanding robust, specific, and stable enzymes. IMPORTANCE This study reveals thatH. volcaniiGK exhibits positive cooperativity for glycerol, ATP, and Mg² + , a kinetic feature not previously reported for glycerol kinases. This behavior enables steep, switch-like responses to small substrate changes, offering unique advantages for biosensor design. Importantly,H. volcaniiGK also maintains high activity under extreme salinity, temperature, broad pH, and solvent conditions that typically limit enzyme use in industrial and environmental applications. These traits make this GK an ideal candidate for enzyme-based biosensors, which often suffer from poor tolerance to pH, solvent, and thermal stress. Its robustness supports its use in cross-linked enzyme crystals, an immobilization method that enhances enzyme stability and reusability under harsh conditions. Moreover, GKs are already employed in Mg² + detection kits; however,H. volcaniiGK’s ability to tolerate and respond to diverse divalent cations (e.g., Co² + , Mn² + ) broadens their potential for pollutant detection and environmental monitoring. These features collectively positionH. volcaniiGK as a valuable biocatalyst for biosensing,in vitrodiagnostics, and biotechnological applications requiring both precision and durability.