Interlocking G-Quadruplexes Using a G-Triad•G Connection: Implications for G-Wire Assembly.

G-quadruplexes are noncanonical structures of nucleic acids formed mainly by G-rich sequences and play crucial roles in important cellular processes. They are also increasingly used in nanotechnology for their valuable properties. Various unexpected structures of G-quadruplexes have been solved recently, including a stable G-quadruplex lacking one guanine in the G-tetrad core, harboring a vacant site. In this study, we demonstrate the interlocking of two intramolecular G-quadruplexes: one containing a vacant site (4n - 1) and the other with an unbound guanine (4n + 1). These G-quadruplexes interact through a G-triad-G connection with unprecedented 5'-3' stacking. Using these interconnection properties, we have identified a sequence capable of self-assembling into G-wires in K+ solutions with potential nanotechnological applications.

Spectroelectrochemical study of carbon structural and functionality characteristics on vanadium redox reactions for flow batteries.

Vanadium redox flow batteries have applications for large-scale electricity storage. This paper reports the influence of carbon structural characteristics of sustainable walnut shell-derived carbons in carbon/polyvinylidene fluoride composite electrodes on vanadium redox reactions. Pyrolysis, gasification, and chemical treatment procedures were used to modify the structural characteristics of carbons. Carbon functional groups were modified by chemical treatment with HNO3, heat treatment with K2CO3, and high-temperature NH3 treatment. Carbon porous structures were characterized using gas adsorption studies. Raman spectroscopy and X-ray diffraction were used to characterize the carbon molecular structure. Functional groups were characterized using X-ray photoelectron spectroscopy, acid/base titrations, temperature-programmed desorption, and Fourier transform infrared spectroscopy. The influence of carbon structure, porosity, and surface functional groups on the redox reactions of vanadium was investigated using cyclic voltammetry and electrical impedance spectroscopy. The VO2+/VO2 + and V2+/V3+ couples had well-defined peaks in cyclic voltammetry, with the former being the most intense, but the V3+/VO2+ couple was not observed for samples carbonized under nitrogen. The results show that V2+/V3+ and VO2+/VO2 + couples observed in cyclic voltammograms were enhanced for carbonization temperatures up to 800 °C. Electrical impedance spectroscopy also showed impedance trends. The electrochemistry results are primarily related to changes in carbon structure and the catalysis of V3+ oxidation by surface functional groups in the carbon structure. The V3+/VO2+ couple was limited by slow kinetics, but it occurs on specific oxygen and nitrogen sites in the carbon structure. The oxidation of V(iii) to V(iv) only occurs on a limited number of surface sites, and the outer-sphere electron transfer to oxidize V(iii) takes place at much more positive potentials. The coulombic, voltage, and energy efficiency of the carbon electrodes were suitable for batteries.

Structural Basis for Parallel G-Quadruplex Recognition by an Ankyrin Protein.

G-Quadruplex (G4) structures formed by guanine-rich DNA and RNA sequences are implicated in various biological processes. Understanding the mechanisms by which proteins recognize G4 structures is crucial for elucidating their functional roles. Here we present the X-ray crystal structure of an ankyrin protein bound to a parallel G4 structure. Our findings reveal a new specific recognition mode in which a bundle of α-helices and loops of the ankyrin form a flat surface to stack on the G-tetrad core. The protein employs a combination of hydrogen bonds and hydrophobic contacts to interact with the G4, and electrostatic interaction is used to enhance the binding affinity. This binding mechanism provides valuable insights into understanding G4 recognition by proteins.

Assessing the potential of Australian indigenous edible halophytes as salt substitutes: From wild to plate.

Increased salt (sodium chloride (NaCl)) consumption contributes to high blood pressure, increasing the risk of cardiovascular disease. Reducing the intake of NaCl could result in significant public health benefits. Australian grown halophytes are consumed traditionally by indigenous communities as food and medicine. The importance of halophytes has been recently "rediscovered" due to their salty taste and crunchy texture. This study aimed to assess the potential of Australian indigenous edible halophytes (AIEH) as salt substitutes. A benchtop test was carried out to establish a sensory lexicon of four important AIEH (samphire, seapurslane, seablite, and saltbush) and to select the most promising halophyte based on sensory attributes and nutritional composition. Samphire and saltbush, the most common and commercially important halophytes, were used as comparisons. Semolina was used to prepare the halophyte-based test food for the benchtop sensory study. Results of the formal sensory study showed that the growing location of samphire and saltbush can significantly affect their sensory attributes. Samphire had the most favorable sensory attributes and nutritional quality, with dry herb and bran aroma and flavor, whereas the saltbush test food preparations had herbaceous, minty dry wood, and green fruit aroma and flavor. The "optimal" concentration of added freeze-dried samphire/saltbush powder was determined based on the saltiness perception of the NaCl-semolina formulation (0.3% table salt equivalent to 1% samphire freeze-dried powder and 1.4%-2.0% saltbush freeze-dried powder, respectively). This study provided novel and crucial information on the potential use of AIEH as natural salt substitutes. PRACTICAL APPLICATION: There is an increasing demand for natural salt substitutes. Halophytes are salt tolerant plants that sustain in arid or semiarid areas and have the potential to be used as natural salt substitutes. To the best of our knowledge, this is the first study reporting the sensory profiles of four important Australian indigenous edible halophytes (samphire, seapurslane, seablite, and saltbush). This study also demonstrated how different growing locations can affect the sensory attributes of halophytes and subsequently their potential food applications. Our findings provide critical information and data to further study halophytes in the context of novel food applications.

A ratiometric fluorescence probe for bisulfite detection in live cells and meat samples.

The development of reliable probe technology for the detection of bisulfite (HSO3-) in situ in food and biological samples is contributing significantly to food quality and safety assurance as well as community health. In this work, a responsive probe, EHDI, is developed for ratiometric fluorescence detection of HSO3- in aqueous solution, meat samples, and living cells. The probe is designed based on the HSO3- triggered 1,4-addition of electron deficit C = C bond of EHDI. As a result of this specific 1,4-addition, the π-conjugation system was destructed, resulting in blue shifts of the emission from 687 to 440 nm and absorption from 577 to 355 nm. The probe has good water solubility, high sensitivity and selectivity, allowing it to be used for imaging of HSO3- internalization and production endogenously. The capability of probe EHDI for HSO3- was then validated by traditional HPLC technology, enabling accurately detect HSO3- in beef samples. The successful development of this probe thus offers a new tool for investigating HSO3- in situ in food and biological conditions.

Layer-by-layer assembly of nanotheranostic particles for simultaneous delivery of docetaxel and doxorubicin to target osteosarcoma.

Osteosarcoma (OS) is a rare form of primary bone cancer, impacting approximately 3.4 × 106 individuals worldwide each year, primarily afflicting children. Given the limitations of existing cancer therapies, the emergence of nanotheranostic platforms has generated considerable research interest in recent decades. These platforms seamlessly integrate therapeutic potential of drug compounds with the diagnostic capabilities of imaging probes within a single construct. This innovation has opened avenues for enhanced drug delivery to targeted sites while concurrently enabling real-time monitoring of the vehicle's trajectory. In this study, we developed a nanotheranostic system employing the layer-by-layer (LbL) technique on a core containing doxorubicin (DOXO) and in-house synthesized carbon quantum dots. By utilizing chitosan and chondroitin sulfate as polyelectrolytes, we constructed a multilayered coating to encapsulate DOXO and docetaxel, achieving a coordinated co-delivery of both drugs. The LbL-functionalized nanoparticles exhibited an approximate size of 150 nm, manifesting a predominantly uniform and spherical morphology, with an encapsulation efficiency of 48% for both drugs. The presence of seven layers in these systems facilitated controlled drug release over time, as evidenced by in vitro release tests. Finally, the impact of the LbL-functionalized nanoparticles was evaluated on U2OS and Saos-2 osteosarcoma cells. The synergistic effect of the two drugs was found to be crucial in inducing cell death, particularly in Saos-2 cells treated with nanoparticles at concentrations higher than 10 µg/ml. Transmission electron microscopy analysis confirmed the internalization of the nanoparticles into both cell types through endocytic mechanisms, revealing an underlying mechanism of necrosis-induced cell death.

In-vitro colonic fermentation of Kakadu plum (Terminalia ferdinandiana) fruit powder: Microbial biotransformation of phenolic compounds and cytotoxicity.

Kakadu plum (Terminalia ferdinandiana) (KP) is an indigenous fruit used as a functional ingredient in powdered form. Three KP doses (1, 2.5 and 5 g) were digested in a dynamic in vitro gut digestion model over 48 h. Faecal water digests from the colonic reactors were assessed for total soluble polyphenols (TSP), ferric reducing antioxidant power (FRAP), phenolic metabolites and short-chain fatty acids (SCFAs). Effects of digests on cell viability were tested against Caco-2 intestinal and HepG2 hepatic cells. All doses of KP fermentation produced castalagin, corilagin, chebulagic acid, chebulinic acid, and gallic acid. TSP and FRAP significantly increased in 5 g KP digests at 0 and 48 h of fermentation. SCFA concentrations significantly increased after 48 h. Cytotoxic effects of 2.5 and 5 g KP digests diminished significantly after 12 h. Overall, colonic fermentation increased antioxidant activity and polyphenolic metabolites of 5 g KP powder for 48 h.

PROM2 overexpression induces metastatic potential through epithelial-to-mesenchymal transition and ferroptosis resistance in human cancers.

INTRODUCTION: Despite considerable therapeutic advances in the last 20 years, metastatic cancers remain a major cause of death. We previously identified prominin-2 (PROM2) as a biomarker predictive of distant metastases and decreased survival, thus providing a promising bio-target. In this translational study, we set out to decipher the biological roles of PROM2 during the metastatic process and resistance to cell death, in particular for metastatic melanoma. METHODS AND RESULTS: Methods and results: We demonstrated that PROM2 overexpression was closely linked to an increased metastatic potential through the increase of epithelial-to-mesenchymal transition (EMT) marker expression and ferroptosis resistance. This was also found in renal cell carcinoma and triple negative breast cancer patient-derived xenograft models. Using an oligonucleotide anti-sense anti-PROM2, we efficaciously decreased PROM2 expression and prevented metastases in melanoma xenografts. We also demonstrated that PROM2 was implicated in an aggravation loop, contributing to increase the metastatic burden both in murine metastatic models and in patients with metastatic melanoma. The metastatic burden is closely linked to PROM2 expression through the expression of EMT markers and ferroptosis cell death resistance in a deterioration loop. CONCLUSION: Our results open the way for further studies using PROM2 as a bio-target in resort situations in human metastatic melanoma and also in other cancer types.

Utilizing 3D Point Cloud Technology with Deep Learning for Automated Measurement and Analysis of Dairy Cows.

This paper introduces an approach to the automated measurement and analysis of dairy cows using 3D point cloud technology. The integration of advanced sensing techniques enables the collection of non-intrusive, precise data, facilitating comprehensive monitoring of key parameters related to the health, well-being, and productivity of dairy cows. The proposed system employs 3D imaging sensors to capture detailed information about various parts of dairy cows, generating accurate, high-resolution point clouds. A robust automated algorithm has been developed to process these point clouds and extract relevant metrics such as dairy cow stature height, rump width, rump angle, and front teat length. Based on the measured data combined with expert assessments of dairy cows, the quality indices of dairy cows are automatically evaluated and extracted. By leveraging this technology, dairy farmers can gain real-time insights into the health status of individual cows and the overall herd. Additionally, the automated analysis facilitates efficient management practices and optimizes feeding strategies and resource allocation. The results of field trials and validation studies demonstrate the effectiveness and reliability of the automated 3D point cloud approach in dairy farm environments. The errors between manually measured values of dairy cow height, rump angle, and front teat length, and those calculated by the auto-measurement algorithm were within 0.7 cm, with no observed exceedance of errors in comparison to manual measurements. This research contributes to the burgeoning field of precision livestock farming, offering a technological solution that not only enhances productivity but also aligns with contemporary standards for sustainable and ethical animal husbandry practices.

Effect of the nature of the solid substrate on spatially heterogeneous activated dynamics in glass forming supported films.

We extend the force-level elastically collective nonlinear Langevin equation theory to treat the spatial gradients of the alpha relaxation time and glass transition temperature, and the corresponding film-averaged quantities, to the geometrically asymmetric case of finite thickness supported films with variable fluid-substrate coupling. The latter typically nonuniversally slows down motion near the solid-liquid interface as modeled via modification of the surface dynamic free energy caging constraints that are spatially transferred into the film and which compete with the accelerated relaxation gradient induced by the vapor interface. Quantitative applications to the foundational hard sphere fluid and a polymer melt are presented. The strength of the effective fluid-substrate coupling has very large consequences for the dynamical gradients and film-averaged quantities in a film thickness and thermodynamic state dependent manner. The interference of the dynamical gradients of opposite nature emanating from the vapor and solid interfaces is determined, including the conditions for the disappearance of a bulk-like region in the film center. The relative importance of surface-induced modification of local caging vs the generic truncation of the long range collective elastic component of the activation barrier is studied. The conditions for the accuracy and failure of a simple superposition approximation for dynamical gradients in thin films are also determined. The emergence of near substrate dead layers, large gradient effects on film-averaged response functions, and a weak non-monotonic evolution of dynamic gradients in thick and cold films are briefly discussed. The connection of our theoretical results to simulations and experiments is briefly discussed, as is the extension to treat more complex glass-forming systems under nanoconfinement.

Effect of Pharmacist-Led Training on Adherence and Practice of Inhaler Use: A Pre-Post Interventional Study in Outpatients With Asthma at Hue University Hospital.

Objective This study aimed to evaluate the impact of a pharmacist-led intervention on improving adherence and practice of inhaler use in outpatients with asthma at a hospital in Vietnam. Methods A pre-post interventional study was conducted at Hue University Hospital. An adapted checklist for both metered-dose inhalers and/or dry powder inhalers was used to evaluate the inhaler technique. Adherence was assessed by using the Test of Adherence to Inhalers questionnaire. The means of interventions comprised "Face-to-face training," "Creating the leaflet for patients," and "Watching guidance video." Results The number of participants with complete data was 79. Before the intervention, 54.4% of patients had misused inhalers, especially inappropriate posture when using devices (70.2%) and not exhaling before inhalation (46.8%). Non-adherence accounted for 55.7% of patients, and the erratic pattern was the highest, with 83.5%. The intervention had remarkably raised the number of good practice and good adherence patients after three months (P < 0.001). Conclusion Pharmacist-led intervention has a positive impact on improving the adherence to inhalers and inhalation techniques of patients with asthma. Practice Implications The pharmacist-led education model could be considered as an effective and feasible solution for asthma management in outpatients and better medication use. Key Points (1) The most frequently observed mistakes in this study were inappropriate posture and inhalation skill when using devices. (2) Pharmacist-led training remarkably improved patients' practice of inhaler use as well as medication adherence.

Genomic and vaccine preclinical studies reveal a novel mouse-adapted Helicobacter pylori model for the hpEastAsia genotype in Southeast Asia.

Introduction. Helicobacter pylori infection is a major global health concern, linked to the development of various gastrointestinal diseases, including gastric cancer. To study the pathogenesis of H. pylori and develop effective intervention strategies, appropriate animal pathogen models that closely mimic human infection are essential.Gap statement. This study focuses on the understudied hpEastAsia genotype in Southeast Asia, a region marked by a high H. pylori infection rate. No mouse-adapted model strains has been reported previously. Moreover, it recognizes the urgent requirement for vaccines in developing countries, where overuse of antimicrobials is fuelling the emergence of resistance.Aim. This study aims to establish a novel mouse-adapted H. pylori model specific to the hpEastAsia genotype prevalent in Southeast Asia, focusing on comparative genomic and histopathological analysis of pathogens coupled with vaccine preclinical studies.Methodology. We collected and sequenced the whole genome of clinical strains of H. pylori from infected patients in Vietnam and performed comparative genomic analyses of H. pylori strains in Southeast Asia. In parallel, we conducted preclinical studies to assess the pathogenicity of the mouse-adapted H. pylori strain and the protective effect of a new spore-vectored vaccine candidate on male Mlac:ICR mice and the host immune response in a female C57BL/6 mouse model.Results. Genome sequencing and comparison revealed unique and common genetic signatures, antimicrobial resistance genes and virulence factors in strains HP22 and HP34; and supported clarithromycin-resistant HP34 as a representation of the hpEastAsia genotype in Vietnam and Southeast Asia. HP34-infected mice exhibited gastric inflammation, epithelial erosion and dysplastic changes that closely resembled the pathology observed in human H. pylori infection. Furthermore, comprehensive immunological characterization demonstrated a robust host immune response, including both mucosal and systemic immune responses. Oral vaccination with candidate vaccine formulations elicited a significant reduction in bacterial colonization in the model.Conclusion. Our findings demonstrate the successful development of a novel mouse-adapted H. pylori model for the hpEastAsia genotype in Vietnam and Southeast Asia. Our research highlights the distinctive genotype and pathogenicity of clinical H. pylori strains in the region, laying the foundation for targeted interventions to address this global health burden.

Understanding the effect of moderate concentration SDS on CO2 hydrates growth in the presence of THF.

Hypothesis Additives like Tetrahydrofuran (THF) and Sodium Dodecylsulfate (SDS) improve Carbon Dioxide (CO2) hydrates thermal stability and growth rate when used separately. It has been hypothesised that combining them could improve the kinetics of growth and the thermodynamic stability of CO2 hydrates. Simulations and Experiments We exploit atomistic molecular dynamics simulations to investigate the combined impact of THF and SDS under different temperatures and concentrations. The simulation insights are verified experimentally using pendant drop tensiometry conducted at ambient pressures and high-pressure differential scanning calorimetry. Findings Our simulations revealed that the combination of both additives is synergistic at low temperatures but antagonistic at temperatures above 274.1 K due to the aggregation of SDS molecules induced by THF molecules. These aggregates effectively remove THF and CO2 from the hydrate-liquid interface, thereby reducing the driving force for hydrates growth. Experiments revealed that the critical micelle concentration of SDS in water decreases by 20% upon the addition of THF. Further experiments in the presence of THF showed that only small amounts of SDS are sufficient to increase the CO2 storage efficiency by over 40% compared to results obtained without promoters. Overall, our results provide microscopic insights into the mechanisms of THF and SDS promoters on CO2 hydrates, useful for determining the optimal conditions for hydrate growth.

Stitched peptides as potential cell permeable inhibitors of oncogenic DAXX protein.

DAXX (Death Domain Associated Protein 6) is frequently upregulated in various common cancers, and its suppression has been linked to reduced tumor progression. Consequently, DAXX has gained significant interest as a therapeutic target in such cancers. DAXX is known to function in several critical biological pathways including chromatin remodelling, transcription regulation, and DNA repair. Leveraging structural information, we have designed and developed a novel set of stapled/stitched peptides that specifically target a surface on the N-terminal helical bundle domain of DAXX. This surface serves as the anchor point for binding to multiple interaction partners, such as Rassf1C, p53, Mdm2, and ATRX, as well as for the auto-regulation of the DAXX N-terminal SUMO interaction motif (SIM). Our experiments demonstrate that these peptides effectively bind to and inhibit DAXX with a higher affinity than the known interaction partners. Furthermore, these peptides release the auto-inhibited SIM, enabling it to interact with SUMO-1. Importantly, we have developed stitched peptides that can enter cells, maintaining their intracellular concentrations at nanomolar levels even after 24 hours, without causing any membrane perturbation. Collectively, our findings suggest that these stitched peptides not only serve as valuable tools for probing the molecular interactions of DAXX but also hold potential as precursors to the development of therapeutic interventions.

RNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms.

The extracellular matrix of bacterial biofilms consists of diverse components including polysaccharides, proteins and DNA. Extracellular RNA (eRNA) can also be present, contributing to the structural integrity of biofilms. However, technical difficulties related to the low stability of RNA make it difficult to understand the precise roles of eRNA in biofilms. Here, we show that eRNA associates with extracellular DNA (eDNA) to form matrix fibres in Pseudomonas aeruginosa biofilms, and the eRNA is enriched in certain bacterial RNA transcripts. Degradation of eRNA associated with eDNA led to a loss of eDNA fibres and biofilm viscoelasticity. Compared with planktonic and biofilm cells, the biofilm matrix was enriched in specific mRNA transcripts, including lasB (encoding elastase). The mRNA transcripts colocalised with eDNA fibres in the biofilm matrix, as shown by single molecule inexpensive FISH microscopy (smiFISH). The lasB mRNA was also observed in eDNA fibres in a clinical sputum sample positive for P. aeruginosa. Thus, our results indicate that the interaction of specific mRNAs with eDNA facilitates the formation of viscoelastic networks in the matrix of Pseudomonas aeruginosa biofilms.

Synthesis of Biodegradable and Antimicrobial Nanocomposite Films Reinforced for Coffee and Agri-Food Product Preservation.

The antimicrobial activity of silver nanoparticles is widely known. However, their application to biodegradable polymeric materials is still limited. In this work, we report a strategy involving the green synthesis of nanocomposite films based on a natural biodegradable matrix. Nanometer-sized silver nanoparticles (C-AgNPs) were synthesized with the aid of ultrasound waves between the silver nitrate solution and the nanocurcumin solution. The green synthesized C-AgNPs were found to have particle sizes in the range of 5-25 nm and demonstrated good antimicrobial activity against Clostridium perfringens, Staphylococcus aureus, Bacillus subtilis, Macrophoma theicola, and Aspergillus flavus. Owing to their physical-chemical and mechanical properties and the excellent antimicrobial activities, the obtained AgNPs were used together with chitosan, cassava starch, and poly(vinyl alcohol) (PVA) to make nanocomposite films, which are suitable for the packaging requirements of various key agricultural and food products such as coffee beans, bamboo straws, and fruits. The nanocomposite films lost up to 85% of their weight after being buried in the soil for 120 days. This indicates that the films made with natural biodegradable materials are environmentally friendly.

Red Blood Cell-Derived Extracellular Vesicles Display Endogenous Antiviral Effects and Enhance the Efficacy of Antiviral Oligonucleotide Therapy.

The COVID-19 pandemic has resulted in a large number of fatalities and, at present, lacks a readily available curative treatment for patients. Here, we demonstrate that unmodified red blood cell-derived extracellular vesicles (RBCEVs) can inhibit SARS-CoV-2 infection in a phosphatidylserine (PS) dependent manner. Using T cell immunoglobulin mucin domain-1 (TIM-1) as an example, we demonstrate that PS receptors on cells can significantly increase the adsorption and infection of authentic and pseudotyped SARS-CoV-2 viruses. RBCEVs competitively inhibit this interaction and block TIM-1-mediated viral entry into cells. We further extend the therapeutic efficacy of this antiviral treatment by loading antisense oligonucleotides (ASOs) designed to target conserved regions of key SARS-CoV-2 genes into RBCEVs. We establish that ASO-loaded RBCEVs are efficiently taken up by cells in vitro and in vivo to suppress SARS-CoV-2 replication. Our findings indicate that this RBCEV-based SARS-CoV-2 therapeutic displays promise as a potential treatment capable of inhibiting SARS-CoV-2 entry and replication.

Automatic Detection and Segmentation of Brain Hemorrhage Based on Improved U-Net Model.

Brain hemorrhage is one of the leading causes of death due to the sudden rupture of a blood vessel in the brain, resulting in bleeding in the brain parenchyma. The early detection and segmentation of brain damage are extremely important for prompt treatment. Some previous studies focused on localizing cerebral hemorrhage based on bounding boxes without specifying specific damage regions. However, in practice, doctors need to detect and segment the hemorrhage area more accurately. In this paper, we propose a method for automatic brain hemorrhage detection and segmentation using the proposed network models, which are improved from the U-Net by changing its backbone with typical feature extraction networks, i.e., DenseNet-121, ResNet-50, and MobileNet-V2. The U-Net architecture has many outstanding advantages. It does not need to do too many preprocessing techniques on the original images and it can be trained with a small dataset providing low error segmentation in medical images. We use the transfer learning approach with the head CT dataset gathered on Kaggle including two classes, bleeding and non-bleeding. Besides, we give some comparison results between the proposed models and the previous works to provide an overview of the suitable model for cerebral CT images. On the head CT dataset, our proposed models achieve a segmentation accuracy of up to 99%.

Dataset of bulged G-quadruplex forming sequences in the human genome.

When several continuous guanine runs are present closely in a nucleic acid sequence, a secondary structure called G-quadruplex can form (G4s). Such structures in the genome could serve as structural and functional regulators in gene expression, DNA-protein binding, epigenetic modification, and genotoxic stress. Several types of G4-forming DNA sequences exist, including bulged G4-forming sequences (G4-BS). Such bulges occur due to the presence of non-guanine bases in specific locations (G-runs) in the G4-forming sequences. At present, search algorithms do not identify stable G4-BS conformations, making genome-wide studies of G4-like structures difficult. Data provided in this study are related to a published article "Stable bulged G-quadruplexes in the human genome: Identification, experimental validation and functionalization" published by Nucleic Acids Research [DIO.org/10.193/nar/gkad252]. Based on our studies in vitro and G4-seq and G4 CUT&Tag data analysis, we have specified and validated three pG4-BS models. In this article, a large collection of 'raw' (unfiltered) dataset is presented, which includes three subfamilies of pG4-BS. For each of pG4-BS, we provide strand-specific genomic boundaries. Data on pG4-BS might be useful in elucidating their structural, functional, and evolutionary roles. Furthermore, they may provide insight into the pathobiology of G4-like structures and their potential therapeutic applications.

Prediction of G4 formation in live cells with epigenetic data: a deep learning approach.

G-quadruplexes (G4s) are secondary structures abundant in DNA that may play regulatory roles in cells. Despite the ubiquity of the putative G-quadruplex-forming sequences (PQS) in the human genome, only a small fraction forms G4 structures in cells. Folded G4, histone methylation and chromatin accessibility are all parts of the complex cis regulatory landscape. We propose an approach for prediction of G4 formation in cells that incorporates epigenetic and chromatin accessibility data. The novel approach termed epiG4NN efficiently predicts cell-specific G4 formation in live cells based on a local epigenomic snapshot. Our results confirm the close relationship between H3K4me3 histone methylation, chromatin accessibility and G4 structure formation. Trained on A549 cell data, epiG4NN was then able to predict G4 formation in HEK293T and K562 cell lines. We observe the dependency of model performance with different epigenetic features on the underlying experimental condition of G4 detection. We expect that this approach will contribute to the systematic understanding of correlations between structural and epigenomic feature landscape.