G-quadruplexes (G4s) are non-canonical secondary nucleic acid structures. Sequences with the potential to form G4s are abundant in regulatory regions of the genome including telomeres, promoters and 5′ non-coding regions, indicating they fulfill important genome regulatory functions. Generally, G4s perform various biological functions by interacting with proteins. In recent years, an increasing number of G-quadruplex-binding proteins have been identified with biochemical experiments. G4-binding proteins are involved in vital cellular processes such as telomere maintenance, DNA replication, gene transcription, mRNA processing. Therefore, G4-binding proteins are also associated with various human diseases. An intensive study of G4-protein interactions provides an attractive approach for potential therapeutics and these proteins can be considered as drug targets for novel medical treatment. In this review, we present biological functions and structural properties of G4-binding proteins, and discuss how to exploit G4-protein interactions to develop new therapeutic targets.

The female reproductive system represents a highly complex regulatory network governing critical physiological functions, encompassing reproductive capacity and endocrine regulation that maintains female physiological homeostasis. The in vitro simulation system provides a novel tool for biomedical research and can be used as physiological and pathological models to study the female reproductive system. Recent advances in this technology have evolved from 2D and 3D printing to organ-on-a-chip (OOC) and microfluidic systems, which has emerged as a transformative platform for modeling the female reproductive system. These microphysiological systems integrate microfluidics, 3D cell culture, and biomimetic scaffolds to replicate key functional aspects of reproductive organs and tissues. They have enabled precise simulation of hormonal regulation, embryo-endometrium interactions, and disease mechanisms such as endometriosis and gynecologic cancers. This review highlights the current state of female reproductive OOCs, including ovary-, uterus-, and fallopian tube-on-a-chip system, their applications in assisted reproduction and disease modeling, and the technological hurdles to their widespread application. Though significant barriers remain in scaling OOCs for high-throughput drug screening, standardizing protocols for clinical applications, and validating their predictive value against human patient outcomes, OOCs have emerged as a transformative platform to model complex pathologies, offering unprecedented insights into disease mechanisms and personalized therapeutic interventions. Future directions, including multi-organ integration for systemic reproductive modeling, incorporation of microbiome interactions, and clinical translation for mechanisms of drug action, will facilitate unprecedented insights into reproductive physiology and pathology.

G-quadruplex (G4) structures are critical epigenetic regulatory elements, which usually form in guanine-rich regions in DNA. However, predicting the formation of G4 structures within living cells remains a challenge. Here, we present an ultra-robust machine learning method, G4Beacon, which utilizes the Gradient-Boosting Decision Tree (GBDT) algorithm, coupled with the ATAC-seq data and the surrounding sequences of in vitro G4s, to accurately predict the formation ability of these in vitro G4s in different cell types. As a result, our model achieved excellent performance even when the test set was extremely skewed. Besides this, G4Beacon can also identify the in vivo G4s of other cell lines precisely with the model built on a special cell line, regardless of the experimental techniques or platforms. Altogether, G4Beacon is an accurate, reliable, and easy-to-use method for the prediction of in vivo G4s of various cell lines.

Microorganisms can transfer electrons directly to extracellular acceptors, during which organic compounds are oxidized to carbon dioxide. One of these microbes, Geobacter sulfurreducens, is well known for the “metallic-like” conductivity of its type IV pili. However, there is no consensus on what the mechanism for electron transfer along these conductive pili is. Based on the aromatic distances and orientations of our predicted models, the mechanism of electron transfer in the Geobacter sulfurreducens (GS) pili was explored by quantum chemical calculations with Marcus theory of electron transfer reactions. Three aromatic residues from the N-terminal α-helix of the GS pilin subunit are packed together, resulting in a continuous pi-pi interaction chain. The theoretical conductance (4.69 μS/3.85 μS) of the predicted models is very similar to that in the experiments reported recently (3.40 μS). These findings offer a new concept that the GS pili belongs to a new class of proteins that can transport electrons through pi-pi interaction between aromatic residues and also provide a valuable tool for guiding further researches of these conductive pili, to investigate their roles in biogeochemical cycling, and potential applications in biomaterials, bioelectronics, and bioenergy.

G-quadruplexes (G4s) are guanine-rich DNA secondary structures with known regulatory roles in eukaryotes, but their functions in bacteria remain largely unexplored. Here, we systematically analyzed potential G-quadruplexes (PG4s) across 1566 bacterial genomes. PG4s showed non-random distributions, with strong enrichment in intergenic regions, particularly near gene start sites, suggesting potential roles in transcriptional regulation. Structural analysis revealed a higher proportion of short-loop G4s in these regions, indicating enhanced stability. Comparisons with randomized genomes confirmed that the observed patterns cannot be explained by GC content or genome size alone. Ecological analysis further revealed that bacteria associated with homothermic hosts exhibit significantly lower G4 densities than free-living species, suggesting reduced reliance on G4-mediated regulation in stable environments. Together, these findings highlight G4s as conserved yet context-dependent elements of bacterial genome organization and provide new insights into their potential regulatory roles in prokaryotes.

Background: G-quadruplexes (G4s) are non-canonical higher-order nucleic acid structures that form at guanine-rich motifs, with features spanning both secondary and tertiary structural levels. These dynamic structures play pivotal roles in diverse cellular processes. Endogenous G4s (eG4s) function through their dynamically formed structures, prompting the hypothesis that their thermostability, as a key structural property, may critically influence their functionality. This study investigates the relationship between G4 stability and other functional genomic signals within eG4 regions and examines its broader impact on chromatin organization and transcriptional regulation. Methods: We developed a mapping strategy to associate in vitro-derived thermostability metrics and multi-omics functional signals with eG4 regions. A stability-centric analytical framework combining correlation analysis and causal inference using the Bayesian networks was applied to decipher causal relationships between G4 stability and the other related signals. We further analyzed the association between the stability of transcription start site (TSS)-proximal eG4s and the biological functions of their downstream genes. Results: Our analyses demonstrate that G4 thermostability exerts causal effects on epigenetic states and transcription factor binding, thereby influencing chromatin and transcription regulation. We further show distinct network architectures for G4-binding versus non-binding transcription factors. Additionally, we find that TSS-proximal eG4s are enriched in genes involved in core proliferation and stress-response pathways, suggesting that eG4s may serve as regulatory elements facilitating rapid stress responses through genome-wide coordination. Conclusions: These findings establish thermostability—though measured in vitro—as an intrinsic property that shapes eG4 functionality. Our study not only provides novel insights into the functional relevance of G4 thermostability but also introduces a generalizable framework for high-throughput G4 data interpretation, significantly advancing the functional decoding of eG4s across biological contexts.