Cohesin-mediated 3D contacts tune enhancer-promoter regulation.

Enhancers are key drivers of gene regulation thought to act via 3D physical interactions with the promoters of their target genes. However, genome-wide depletions of architectural proteins such as cohesin result in only limited changes in gene expression, despite a loss of contact domains and loops. Consequently, the role of cohesin and 3D contacts in enhancer function remains debated. Here, we developed CRISPRi of regulatory elements upon degron operation (CRUDO), a novel approach to measure how changes in contact frequency impact enhancer effects on target genes by perturbing enhancers with CRISPRi and measuring gene expression in the presence or absence of cohesin. We systematically perturbed all 1,039 candidate enhancers near five cohesin-dependent genes and identified 34 enhancer-gene regulatory interactions. Of 26 regulatory interactions with sufficient statistical power to evaluate cohesin dependence, 18 show cohesin-dependent effects. A decrease in enhancer-promoter contact frequency upon removal of cohesin is frequently accompanied by a decrease in the regulatory effect of the enhancer on gene expression, consistent with a contact-based model for enhancer function. However, changes in contact frequency and regulatory effects on gene expression vary as a function of distance, with distal enhancers (e.g., >50Kb) experiencing much larger changes than proximal ones (e.g., <50Kb). Because most enhancers are located close to their target genes, these observations can explain how only a small subset of genes - those with strong distal enhancers - are sensitive to cohesin. Together, our results illuminate how 3D contacts, influenced by both cohesin and genomic distance, tune enhancer effects on gene expression.

Adsorption, Orientation, and Speciation of Amino Acids at Air-Aqueous Interfaces for the Direct Air Capture of CO2.

Amino acids make up a promising family of molecules capable of direct air capture (DAC) of CO2 from the atmosphere. Under alkaline conditions, CO2 reacts with the anionic form of an amino acid to produce carbamates and deactivated zwitterionic amino acids. The presence of the various species of amino acids and reactive intermediates can have a significant effect on DAC chemistry, the role of which is poorly understood. In this study, all-atom molecular dynamics (MD) based computational simulations and vibrational sum frequency generation (vSFG) spectroscopy studies were conducted to understand the role of competitive interactions at the air-aqueous interface in the context of DAC. We find that the presence of potassium bicarbonate ions, in combination with the anionic and zwitterionic forms of amino acids, induces concentration and charge gradients at the interface, generating a layered molecular arrangement that changes under pre- and post-DAC conditions. In parallel, an enhancement in the surface activity of both anionic and zwitterionic forms of amino acids is observed, which is attributed to enhanced interfacial stability and favorable intermolecular interactions between the adsorbed amino acids in their anionic and zwitterionic forms. The collective influence of these competitive interactions, along with the resulting interfacial heterogeneity, may in turn affect subsequent capture reactions and associated rates. These effects underscore the need to consider dynamic changes in interfacial chemical makeup to enhance DAC efficiency and to develop successful negative emission and storage technologies.

Physicochemical control of solvation and molecular assembly of charged amphiphilic oligomers at air-aqueous interfaces.

HYPOTHESIS: Understanding the rules that control the assembly of nanostructured soft materials at interfaces is central to many applications. We hypothesize that electrolytes can be used to alter the hydration shell of amphiphilic oligomers at the air-aqueous interface of Langmuir films, thereby providing a means to control the formation of emergent nanostructures. EXPERIMENTS: Three representative salts - (NaF, NaCl, NaSCN) were studied for mediating the self-assembly of oligodimethylsiloxane methylimidazolium (ODMS-MIM+) amphiphiles in Langmuir films. The effects of the different salts on the nanostructure assembly of these films were probed using vibrational sum frequency generation (SFG) spectroscopy and Langmuir trough techniques. Experimental data were supported by atomistic molecular dynamic simulations. FINDINGS: Langmuir trough surface pressure - area isotherms suggested a surprising effect on oligomer assembly, whereby the presence of anions affects the stability of the interfacial layer irrespective of their surface propensities. In contrast, SFG results implied a strong anion effect that parallels the surface activity of anions. These seemingly contradictory trends are explained by anion driven tail dehydration resulting in increasingly heterogeneous systems with entangled ODMS tails and appreciable anion penetration into the complex interfacial layer comprised of headgroups, tails, and interfacial water molecules. These findings provide physical and chemical insight for tuning a wide range of interfacial assemblies.

Multicenter integrated analysis of noncoding CRISPRi screens.

The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE-gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome.

Towards Energy-Efficient Direct Air Capture with Photochemically-Driven CO2 Release and Solvent Regeneration.

The intensive energy demands associated with solvent regeneration and CO2 release in current direct air capture (DAC) technologies makes their deployment at the massive scales (GtCO2/year) required to positively impact the climate economically unfeasible. This challenge underscores the critical need to develop new DAC processes with significantly reduced energy costs. Recently, we developed a new approach to photochemically drive efficient release of CO2 through an intermolecular proton transfer reaction by exploiting the unique properties of an indazole metastable-state photoacid (mPAH), opening a new avenue towards energy efficient on-demand CO2 release and solvent regeneration using abundant solar energy instead of heat. In this Concept Article, we will describe the principle of our photochemically-driven CO2 release approach for solvent-based DAC systems, discuss the essential prerequisites and conditions to realize this cyclable CO2 release chemistry under ambient conditions. We outline the key findings of our approach, discuss the latest developments from other research laboratories, detail approaches used to monitor DAC systems in situ, and highlight experimental procedures for validating its feasibility. We conclude with a summary and outlook into the immediate challenges that must be addressed in order to fully exploit this novel photochemically-driven approach to DAC solvent regeneration.

Synergistic Assembly of Charged Oligomers and Amino Acids at the Air-Water Interface: An Avenue toward Surface-Directed CO2 Capture.

Interfaces are considered a major bottleneck in the capture of CO2 from air. Efforts to design surfaces to enhance CO2 capture probabilities are challenging due to the remarkably poor understanding of chemistry and self-assembly taking place at these interfaces. Here, we leverage surface-specific vibrational spectroscopy, Langmuir trough techniques, and simulations to mechanistically elucidate how cationic oligomers can drive surface localization of amino acids (AAs) that serve as CO2 capture agents speeding up the apparent rate of absorption. We demonstrate how tuning these interfaces provides a means to facilitate CO2 capture chemistry to occur at the interface, while lowering surface tension and improving transport/reaction probabilities. We show that in the presence of interfacial AA-rich aggregates, one can improve capture probabilities vs that of a bare interface, which holds promise in addressing climate change through the removal of CO2 via tailored interfaces and associated chemistries.

Single-molecule chromatin configurations link transcription factor binding to expression in human cells.

The binding of multiple transcription factors (TFs) to genomic enhancers activates gene expression in mammalian cells. However, the molecular details that link enhancer sequence to TF binding, promoter state, and gene expression levels remain opaque. We applied single-molecule footprinting (SMF) to measure the simultaneous occupancy of TFs, nucleosomes, and components of the transcription machinery on engineered enhancer/promoter constructs with variable numbers of TF binding sites for both a synthetic and an endogenous TF. We find that activation domains enhance a TF's capacity to compete with nucleosomes for binding to DNA in a BAF-dependent manner, TF binding on nucleosome-free DNA is consistent with independent binding between TFs, and average TF occupancy linearly contributes to promoter activation rates. We also decompose TF strength into separable binding and activation terms, which can be tuned and perturbed independently. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the binding microstates observed at the enhancer and subsequent time-dependent gene expression. This work provides a template for quantitative dissection of distinct contributors to gene activation, including the activity of chromatin remodelers, TF activation domains, chromatin acetylation, TF concentration, TF binding affinity, and TF binding site configuration.

Unravelling photoisomerization dynamics in a metastable-state photoacid.

Direct access to trans-cis photoisomerization in a metastable state photoacid (mPAH) remains challenging owing to the presence of competing excited-state relaxation pathways and multiple transient isomers with overlapping spectra. Here, we reveal the photoisomerization dynamics in an indazole mPAH using time-resolved fluorescence (TRF) spectroscopy by exploiting a unique property of this mPAH having fluorescence only from the trans isomer. The combination of these experimental results with time-dependent density function theory (TDDFT) calculations enables us to gain mechanistic insight into this key dynamical process.

Severe obesity in total knee arthroplasty occurs in younger patients with a greater healthcare burden and complication rate.

BACKGROUND: Knee osteoarthritis in the presence of severe obesity (BMI ≥ 40) is becoming an increasing presentation to healthcare services. When progressing to arthroplasty, this group is known to have higher complication rates. METHOD: A retrospective cohort study at a tertiary referral centre (UK) with all sequential patients undergoing TKA between 2019 and 2020 included following identification from the UK National Joint Registry. Patients were divided by BMI < 40 and BMI ≥ 40 (86, 16.3%). Analysis of BMI with pre-operative parameters including age, ASA, and blood parameters was performed. Primary outcome was re-operation rate. Secondary outcomes included length of stay, complications, and re-admission. RESULTS: Five hundred and twenty-eight sequential TKA patients were included. The BMI < 40 group (442 patients, 83.7%) were mean 5.4 years younger (p < 0.001), had a higher ASA grade (p < 0.001) lower albumin (p < 0.001) and higher HbA1c (p < 0.001) than the BMI ≥ 40 group (86 patients, 16.3%). The BMI ≥ 40 group had a higher rate of re-operation (8% vs 2%, p = 0.012), and longer length of stay (mean 1.2 days longer p < 0.001), most commonly due to wound discharge, which alongside dehiscence was significantly higher (11.6% vs 4.3% p = 0.02). Overall, re-admission rates were also higher (18.6% vs 6.1% p = 0.06) with wound dehiscence, superficial infection, and deep infection the most common causes. CONCLUSIONS: Those patients undergoing TKA with a BMI ≥ 40 are younger and have higher reoperation rates, greater length of stay, higher re-admission rates and more postoperative complications, providing a target for the development of pre-operative optimisation programmes.

The landscape of the histone-organized chromatin of Bdellovibrionota bacteria.

Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription and three-dimensional genome organization in a member of Bdellovibrionota (a Bacteriovorax strain). We find that, similar to what is observed in some archaea and in eukaryotes with compact genomes such as yeast, Bacteriovorax chromatin is characterized by preferential accessibility around promoter regions. Similar to eukaryotes, chromatin accessibility in Bacteriovorax positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that unlike in yeast, but similar to the state of mammalian and fly promoters, Bacteriovorax promoters exhibit very strong polymerase pausing. Finally, similar to that of other bacteria without histones, the Bacteriovorax genome exists in a three-dimensional (3D) configuration organized by the parABS system along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the functional diversity in chromatin organization across the tree of life.

An encyclopedia of enhancer-gene regulatory interactions in the human genome.

Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the impact of human genetic variation on disease1-6. Here we create and evaluate a resource of >13 million enhancer-gene regulatory interactions across 352 cell types and tissues, by integrating predictive models, measurements of chromatin state and 3D contacts, and largescale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,411 elementgene pairs measured in CRISPR perturbation experiments, >30,000 fine-mapped eQTLs, and 569 fine-mapped GWAS variants linked to a likely causal gene. Using this framework, we develop a new predictive model, ENCODE-rE2G, that achieves state-of-the-art performance across multiple prediction tasks, demonstrating a strategy involving iterative perturbations and supervised machine learning to build increasingly accurate predictive models of enhancer regulation. Using the ENCODE-rE2G model, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, which reveals global properties of enhancer networks, identifies differences in the functions of genes that have more or less complex regulatory landscapes, and improves analyses to link noncoding variants to target genes and cell types for common, complex diseases. By interpreting the model, we find evidence that, beyond enhancer activity and 3D enhancer-promoter contacts, additional features guide enhancerpromoter communication including promoter class and enhancer-enhancer synergy. Altogether, these genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models, and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics.

Single-cell chromatin state transitions during epigenetic memory formation.

Repressive chromatin modifications are thought to compact chromatin to silence transcription. However, it is unclear how chromatin structure changes during silencing and epigenetic memory formation. We measured gene expression and chromatin structure in single cells after recruitment and release of repressors at a reporter gene. Chromatin structure is heterogeneous, with open and compact conformations present in both active and silent states. Recruitment of repressors associated with epigenetic memory produces chromatin compaction across 10-20 kilobases, while reversible silencing does not cause compaction at this scale. Chromatin compaction is inherited, but changes molecularly over time from histone methylation (H3K9me3) to DNA methylation. The level of compaction at the end of silencing quantitatively predicts epigenetic memory weeks later. Similarly, chromatin compaction at the Nanog locus predicts the degree of stem-cell fate commitment. These findings suggest that the chromatin state across tens of kilobases, beyond the gene itself, is important for epigenetic memory formation.

Cations Control Lipid Bilayer Memcapacitance Associated with Long-Term Potentiation.

Phospholipid bilayers can be described as capacitors whose capacitance per unit area (specific capacitance, Cm) is determined by their thickness and dielectric constant─independent of applied voltage. It is also widely assumed that the Cm of membranes can be treated as a "biological constant". Recently, using droplet interface bilayers (DIBs), it was shown that zwitterionic phosphatidylcholine (PC) lipid bilayers can act as voltage-dependent, nonlinear memory capacitors, or memcapacitors. When exposed to an electrical "training" stimulation protocol, capacitive energy storage in lipid membranes was enhanced in the form of long-term potentiation (LTP), which enables biological learning and long-term memory. LTP was the result of membrane restructuring and the progressive asymmetric distribution of ions across the lipid bilayer during training, which is analogous, for example, to exponential capacitive energy harvesting from self-powered nanogenerators. Here, we describe how LTP could be produced from a membrane that is continuously pumped into a nonequilibrium steady state, altering its dielectric properties. During this time, the membrane undergoes static and dynamic changes that are fed back to the system's potential energy, ultimately resulting in a membrane whose modified molecular structure supports long-term memory storage and LTP. We also show that LTP is very sensitive to different salts (KCl, NaCl, LiCl, and TmCl3), with LiCl and TmCl3 having the most profound effect in depressing LTP, relative to KCl. This effect is related to how the different cations interact with the bilayer zwitterionic PC lipid headgroups primarily through electric-field-induced changes to the statistically averaged orientations of water dipoles at the bilayer headgroup interface.

Ice Recrystallization Inhibition Activity of Soy Protein Hydrolysates.

Identifying and developing ice recrystallization inhibitors from sustainable food proteins such as soy protein isolate (SPI) can lead to practical applications in both pharmaceutical and food industries. The objective of this study was to investigate the ice recrystallization inhibition (IRI) activity of SPI hydrolysates, and this was achieved by using an IRI activity-guided fractionation approach and relating IRI activity to interfacial molecular activity measured by vibrational sum frequency generation (VSFG). In addition, the impact of molecular weight (MW) and enzyme specificity was analyzed using three different proteases (Alcalase, trypsin, and pancreatin) and varying hydrolysis times. Using preparative chromatography, hydrolysates from each enzyme treatment were fractionated into five different MW fractions (F1-F5), which were then characterized by high-performance liquid chromatography (HPLC). All SPI hydrolysates had IRI activity, resulting in a 57-29% ice crystal diameter reduction when compared to native SPI. The F1 fraction (of 4-14 kDa) was most effective among all tested hydrolysates, while the lower MW peptide fractions lacked activity. One sample (SPI-ALC 20-F1) had a 52% reduction of ice crystal size at a lower concentration of 2% compared to the typical 4% used. SFG showed a difference in H-bonding and hydrophobic interactions of the molecules on the water/air interface, which may be linked to IRI activity. This study demonstrates for the first time the ability of SPI hydrolysates to inhibit ice crystal growth and the potential application of SFG to study molecular interaction at the interface that may help illustrate the mechanism of action.

Photochemically-Driven CO2 Release Using a Metastable-State Photoacid for Energy Efficient Direct Air Capture.

One of the grand challenges underlying current direct air capture (DAC) technologies relates to the intensive energy cost for sorbent regeneration and CO2 release, making the massive scale (GtCO2 /year) deployment required to have a positive impact on climate change economically unfeasible. This challenge underscores the critical need to develop new DAC processes with substantially reduced regeneration energies. Here, we report a photochemically-driven approach for CO2 release by exploiting the unique properties of an indazole metastable-state photoacid (mPAH). Our measurements on simulated and amino acid-based DAC systems revealed the potential of mPAH to be used for CO2 release cycles by regulating pH changes and associated isomers driven by light. Upon irradiating with moderate intensity light, a ≈55 % and ≈68 % to ≈78 % conversion of total inorganic carbon to CO2 was found for the simulated and amino acid-based DAC systems, respectively. Our results confirm the feasibility of on-demand CO2 release under ambient conditions using light instead of heat, thereby providing an energy efficient pathway for the regeneration of DAC sorbents.

Tracking Molecular Transport Across Oil/Aqueous Interfaces: Insight into "Antagonistic" Binding in Solvent Extraction.

Liquid/liquid (L/L) interfaces play a key, yet poorly understood, role in a range of complex chemical phenomena where time-evolving interfacial structures and transient supramolecular assemblies act as gatekeepers to function. Here, we employ surface-specific vibrational sum frequency generation combined with neutron and X-ray scattering methods to track the transport of dioctyl phosphoric acid (DOP) and di-(2-ethylhexyl) phosphoric acid (DEHPA) ligands used in solvent extraction at buried oil/aqueous interfaces away from equilibrium. Our results show evidence for a dynamic interfacial restructuring at low ligand concentrations in contrast to expectation. These time-varying interfaces arise from the transport of sparingly soluble interfacial ligands into the neighboring aqueous phase. These results support a proposed "antagonistic" role of ligand complexation in the aqueous phase that could serve as a holdback mechanism in kinetic liquid extractions. These findings provide new insights into interfacially controlled chemical transport at L/L interfaces and how these interfaces vary chemically, structurally, and temporally in a concentration-dependent manner and present potential avenues to design selective kinetic separations.

Chemical Feedback in the Self-Assembly and Function of Air-Liquid Interfaces: Insight into the Bottlenecks of CO2 Direct Air Capture.

As fossil fuels remain a major source of energy throughout the world, developing efficient negative emission technologies, such as direct air capture (DAC), which remove carbon dioxide (CO2) from the air, becomes critical for mitigating climate change. Although all DAC processes involve CO2 transport from air into a sorbent/solvent, through an air-solid or air-liquid interface, the fundamental roles the interfaces play in DAC remain poorly understood. Herein, we study the interfacial behavior of amino acid (AA) solvents used in DAC through a combination of vibrational sum frequency generation spectroscopy and molecular dynamics simulations. This study revealed that the absorption of atmospheric CO2 has antagonistic effects on subsequent capture events that are driven by changes in bulk pH and specific ion effects that feedback on surface organization and interactions. Among the three AAs (leucine, valine, and phenylalanine) studied, we identify and separate behaviors from CO2 loading, chemical changes, variations in pH, and specific ion effects that tune structural and chemical degrees of freedom at the air-aqueous interface. The fundamental mechanistic findings described here are anticipated to enable new approaches to DAC based on exploiting interfaces as a tool to address climate change.

Assembly of polyelectrolyte star block copolymers at the oil-water interface.

To understand and resolve adsorption, reconfiguration, and equilibrium conformations of charged star copolymers, we carried out an integrated experimental and coarse-grained molecular dynamics simulation study of the assembly process at the oil-water interface. This is important to guide development of novel surfactants or amphiphiles for chemical transformations and separations. The star block copolymer consisted of arms that are comprised of hydrophilic-hydrophobic block copolymers that are covalently tethered via the hydrophobic blocks to one point. The hydrophobic core represents polystyrene (PS) chains, while the hydrophilic corona represents quaternized poly(2-vinylpyridine) (P2VP) chains. The P2VP is modeled to become protonated when in contact with an acidic aqueous phase, thereby massively increasing the hydrophilicity of this block, and changing the nature of the star at the oil-water interface. This results in a configurational change whereby the chains comprising the hydrophilic corona are significantly stretched into the aqueous phase, while the hydrophobic core remains solubilized in the oil phase. In the simulations, we followed the kinetics of the anchoring and assembly of the star block copolymer at the interface, monitoring the lateral assembly, and the subsequent reconfiguration of the star via changes in the interfacial tension that varies as the degree-of-protonation increases. At low fractions of protonation, the arm cannot fully partition into the aqueous side of the interface and instead interacts with other arms in the oil phase forming a network near the interface. These insights were used to interpret the non-monotonic dependence of pH with the asymptotic interfacial tension from pendant drop tensiometry experiments and spectral signatures of aromatic stretches seen in vibrational sum frequency generation (SFG) spectroscopy. We describe the relationship of interfacial tension to the star assembly via the Frumkin isotherm, which phenomenologically describes anti-cooperativity in adsorbing stars to the interface due to crowding. Although our model explicitly considers long-range electrostatics, the contribution of electrostatics to interfacial tension is small and brought about by strong counterion condensation at the interface. These results provide key insights into resolving the adsorption, reconfiguration, and equilibrium conformations of charged star block copolymers as surfactants.

Rewriting regulatory DNA to dissect and reprogram gene expression.

Regulatory DNA sequences within enhancers and promoters bind transcription factors to encode cell type-specific patterns of gene expression. However, the regulatory effects and programmability of such DNA sequences remain difficult to map or predict because we have lacked scalable methods to precisely edit regulatory DNA and quantify the effects in an endogenous genomic context. Here we present an approach to measure the quantitative effects of hundreds of designed DNA sequence variants on gene expression, by combining pooled CRISPR prime editing with RNA fluorescence in situ hybridization and cell sorting (Variant-FlowFISH). We apply this method to mutagenize and rewrite regulatory DNA sequences in an enhancer and the promoter of PPIF in two immune cell lines. Of 672 variant-cell type pairs, we identify 497 that affect PPIF expression. These variants appear to act through a variety of mechanisms including disruption or optimization of existing transcription factor binding sites, as well as creation of de novo sites. Disrupting a single endogenous transcription factor binding site often led to large changes in expression (up to -40% in the enhancer, and -50% in the promoter). The same variant often had different effects across cell types and states, demonstrating a highly tunable regulatory landscape. We use these data to benchmark performance of sequence-based predictive models of gene regulation, and find that certain types of variants are not accurately predicted by existing models. Finally, we computationally design 185 small sequence variants (≤10 bp) and optimize them for specific effects on expression in silico. 84% of these rationally designed edits showed the intended direction of effect, and some had dramatic effects on expression (-100% to +202%). Variant-FlowFISH thus provides a powerful tool to map the effects of variants and transcription factor binding sites on gene expression, test and improve computational models of gene regulation, and reprogram regulatory DNA.