Explore the vast range of titles available.

Key Points Epigenetic profiling has been extensively undertaken in different systems, including development and disease. However, functional characterization of the dynamics of epigenomes, which will provide mechanistic insights into the role of epigenetics in diverse biological systems, remains largely unexplored. Proteins with a methyl-CpG binding domain (MBD) are well-studied readers and effectors of DNA methylation. Transcription factors (TFs) are now emerging as a new class of DNA methylation readers and effectors that translate DNA methylation signals into biological actions. Different high-throughput approaches, including tandem mass spectrometry (MS/MS), protein microarray, DNA microarray and chromatin immunoprecipitation followed by bisulfite sequencing (ChIP–BS-seq), have identified almost 100 TFs that interact with methylated DNA in vitro . A few of these have been confirmed to bind methylated DNA in vivo . Two models may explain the relationship between TF binding and DNA methylation. Although some TFs can affect the DNA methylation status at the genomic regions near their binding sites, the interaction of other TFs with DNA is dependent on DNA methylation within their respective binding sites. The interactions between TFs and methylated DNA could impact various processes, including gene expression regulation, splicing regulation, chromatin remodelling and disease. Besides conventional CpG methylation, non-CpG methylation and other methylation derivatives (including 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC)), have also been profiled in different cell types. Many proteins found to interact with these modifications were determined to be TFs. Evidence is emerging that transcription factors (TFs) lacking methyl-CpG binding domains can interact with methylated DNA. This Analysis article reviews the in vitro and in vivo evidence for methylation-mediated interactions between TFs and DNA, and their functional consequences. Recent technological advances have made it possible to decode DNA methylomes at single-base-pair resolution under various physiological conditions. Many aberrant or differentially methylated sites have been discovered, but the mechanisms by which changes in DNA methylation lead to observed phenotypes, such as cancer, remain elusive. The classical view of methylation-mediated protein–DNA interactions is that only proteins with a methyl-CpG binding domain (MBD) can interact with methylated DNA. However, evidence is emerging to suggest that transcription factors lacking a MBD can also interact with methylated DNA. The identification of these proteins and the elucidation of their characteristics and the biological consequences of methylation-dependent transcription factor–DNA interactions are important stepping stones towards a mechanistic understanding of methylation-mediated biological processes, which have crucial implications for human development and disease.

Fibrotic skin disease represents a major global healthcare burden, characterized by fibroblast hyperproliferation and excessive accumulation of extracellular matrix. Fibroblasts are found to be heterogeneous in multiple fibrotic diseases, but fibroblast heterogeneity in fibrotic skin diseases is not well characterized. In this study, we explore fibroblast heterogeneity in keloid, a paradigm of fibrotic skin diseases, by using single-cell RNA-seq. Our results indicate that keloid fibroblasts can be divided into 4 subpopulations: secretory-papillary, secretory-reticular, mesenchymal and pro-inflammatory. Interestingly, the percentage of mesenchymal fibroblast subpopulation is significantly increased in keloid compared to normal scar. Functional studies indicate that mesenchymal fibroblasts are crucial for collagen overexpression in keloid. Increased mesenchymal fibroblast subpopulation is also found in another fibrotic skin disease, scleroderma, suggesting this is a broad mechanism for skin fibrosis. These findings will help us better understand skin fibrotic pathogenesis, and provide potential targets for fibrotic disease therapies. Fibroblasts are found to be heterogeneous in multiple fibrotic diseases, but fibroblast heterogeneity in fibrotic skin diseases is not well characterized. Here the authors employ scRNA-seq to explore fibroblast heterogeneity in keloid, a paradigm of fibrotic skin diseases.

Accurate identification of protein function is critical to elucidate life mechanisms and design new drugs. We proposed a novel deep-learning method, ATGO, to predict Gene Ontology (GO) attributes of proteins through a triplet neural-network architecture embedded with pre-trained language models from protein sequences. The method was systematically tested on 1068 non-redundant benchmarking proteins and 3328 targets from the third Critical Assessment of Protein Function Annotation (CAFA) challenge. Experimental results showed that ATGO achieved a significant increase of the GO prediction accuracy compared to the state-of-the-art approaches in all aspects of molecular function, biological process, and cellular component. Detailed data analyses showed that the major advantage of ATGO lies in the utilization of pre-trained transformer language models which can extract discriminative functional pattern from the feature embeddings. Meanwhile, the proposed triplet network helps enhance the association of functional similarity with feature similarity in the sequence embedding space. In addition, it was found that the combination of the network scores with the complementary homology-based inferences could further improve the accuracy of the predicted models. These results demonstrated a new avenue for high-accuracy deep-learning function prediction that is applicable to large-scale protein function annotations from sequence alone.

Background/Aims: MicroRNAs (miRNAs, miRs) have emerged as important post-transcriptional regulators in various cancers. miR-543 has been reported to play critical roles in hepatocellular carcinoma and colorectal cancer, however, the role of miR-543 in the pathogenesis of prostate cancer has not been fully understood. Methods: Expression of miR-543 and Raf Kinase Inhibitory Protein (RKIP) in clinical prostate cancer specimens, two prostate cancer cell lines, namely LNCAP and C4-2B, were determined. The effects of miR-543 on proliferation and metastasis of tumor cells were also investigated with both in vitro and in vivo studies. Results: miR-543 was found to be negatively correlated with RKIP expression in clinical tumor samples and was significantly upregulated in metastatic prostate cancer cell line C4-2B compared with parental LNCAP cells. Further studies identified RKIP as a direct target of miR-543. Overexpression of miR-543 downregulated RKIP expression and promoted the proliferation and metastasis of cancer cells, whereas knockdown of miR-543 increased expression of RKIP and suppressed the proliferation and metastasis of cancer cells in vitro and in vivo. Conclusion: Our study demonstrates that miR-543 promotes the proliferation and metastasis of prostate cancer via targeting RKIP.

A comprehensive study was undertaken at Jiaozi coal mine to investigate the development regularity of ground fissures in shallow buried coal seam mining with Karst landform, shedding light on the development type, geographical distribution, dynamic development process, and failure mechanism of these ground fissures by employing field monitoring, numerical simulation, and theoretical analysis. The findings demonstrate that ground fissure development has an obvious feature of subregion, and its geographical distribution is significantly affected by topography. Tensile type, open type, and stepped type are three different categories of ground fissure. Ground fissures emerge dynamically as the panel advances, and they typically develop with a distance of less than periodic weighting step distance in advance of panel advancing position. Ground fissures present the dynamic development feature, temporary fissure has the ability of self-healing. The dynamic development process of ground fissure with closed-distance coal seam repeated mining is expounded, and the development scale is a dynamic development stage of “closure → expansion → stabilized” on the basis of the original development scale. From the perspective of topsoil deformation, the computation model considering two points movement vectors towards two directions of the gob and the ground surface is established, the development criterion considering the critical deformation value of topsoil is obtained. The mechanical model of hinged structure of inclined body is proposed to clarify the ground fissure development, and the interaction between slope activity and ground fissure development is expounded. These research results fulfill the gap of ground fissures about development regularity and formation mechanism, and can contribute to ground fissure prevention and treatment with Karst landform.

This study, based on the criteria of “inclusiveness,” “sustainability,” and “internal-external structural coordination,” establishes an evaluative framework for appraising the high-quality development of the insurance sector. It systematically gauges the overarching high-quality developmental status of China’s insurance industry across regions. Employing non-parametric kernel density estimation, the Standard Deviation Ellipse, and spatial Markov chain, the investigation dynamically scrutinizes the national landscape of high-quality evolution within the insurance sector over the temporal spectrum. Furthermore, Moran’s index and Dagum’s Gini coefficient are harnessed to disentangle the spatial interdependence and heterogeneity characterizing the high-quality progression of the insurance industry among provinces. The findings disclose a pronounced regional development gap throughout China, surpassing intra-regional disparities and underscoring a notable concern of imbalance in regional insurance industry development. Despite the elevated development stature of the eastern region, substantial interprovincial differentials persist, exposing internal “inequities” within this region. In the central and western domains, although internal divergences in insurance industry development are gradually diminishing, the overall developmental benchmarks remain comparatively subdued.

Water electro-oxidation to form H 2 O 2 is an important way to produce H 2 O 2 which is widely applied in industry. However, its mechanism is under debate and HO (ads) , hydroxyl group adsorbed onto the surface of the electrode, is regarded as an important intermediate. Herein, we study the mechanism of water oxidation to H 2 O 2 at Pt electrode using in-situ Raman spectroscopy and differential electrochemical mass spectroscopy and find peroxide bond mainly originated from the coupling of two CO 3 2- via a C 2 O 6 2- intermediate. By quantifying the 18 O isotope in the product, we find that 93% of H 2 O 2 was formed via the CO 3 2- coupling route and 7% of H 2 O 2 is from OH (ads) -CO 3 •− route. The OH (ads) -OH (ads) coupling route has a negligible contribution. The comparison of various electrodes shows that the strong adsorption of CO 3(ads) at the electrode surface is essential. Combining with a commercial cathode catalyst to produce H 2 O 2 during oxygen reduction, we assemble a flow cell in which the cathode and anode simultaneously produce H 2 O 2 . It shows a Faradaic efficiency of 150% of H 2 O 2 at 1 A cm −2 with a cell voltage of 2.3 V. Electrosynthesis via two electron water reactions offers a promising method for decentralized H 2 O 2 production, yet its mechanism remains unclear. Here, the authors address the challenge by using in-situ Raman and DEMS, and demonstrate 93% of H 2 O 2 forms via the carbonate coupling route through a C 2 O 6 2− intermediate.

Pancreatic cancer is a highly lethal disease with a poor prognosis, and existing therapies offer only limited effectiveness. Mutation gene sequencing has shown several gene associations that may account for its carcinogenesis, revealing a promising research direction. Poly (ADP-ribose) polymerase (PARP) inhibitors target tumor cells with a homologous recombination repair (HRR) deficiency based on the concept of synthetic lethality. The most prominent target gene is BRCA, in which mutations were first identified in breast cancer and ovarian cancer. PARP inhibitors can trap the PARP-1 protein at a single-stranded break/DNA lesion and disrupt its catalytic cycle, ultimately leading to replication fork progression and consequent double-strand breaks. For tumor cells with BRCA mutations, HRR loss would result in cell death. Pancreatic cancer has also been reported to have a strong relationship with BRCA gene mutations, which indicates that pancreatic cancer patients may benefit from PARP inhibitors. Several clinical trials are being conducted and have begun to yield results. For example, the POLO (Pancreatic Cancer Olaparib Ongoing) trial has demonstrated that the median progression-free survival was observably longer in the olaparib group than in the placebo group. However, PARP inhibitor resistance has partially precluded their use in clinical applications, and the major mechanism underlying this resistance is the restoration of HRR. Therefore, determining how to use PARP inhibitors in more clinical applications and how to avoid adverse effects, as well as prognosis and treatment response biomarkers, require additional research. This review elaborates on future prospects for the application of PARP inhibitors in pancreatic cancer.

Unlike humans, mouse bone marrow-derived mesenchymal stem cells (MSCs) cannot be easily harvested by adherence to plastic owing to the contamination of cultures by hematopoietic cells. The design of the protocol described here is based on the phenomenon that compact bones abound in MSCs and hematopoietic cells exist in the marrow cavities and the inner interfaces of the bones. The procedure includes flushing bone marrow out of the long bones, digesting the bone chips with collagenase type II, deprivation of the released cells and culturing the digested bone fragments, out of which fibroblast-like cells migrate and grow in the defined medium. The entire technique requires 5 d before the adherent cells are readily passaged. Further identification assays confirm that these cells are MSCs. We provide an easy and reproducible method to harvest mouse MSCs that does not require depletion of hematopoietic cells by sorting or immunomagnetic techniques.

This study maps the DNA methylome profile of adult mouse dentate gyrus neurons at the single-base resolution and finds prevalent methylation of both CpG dinucleotides and non-CpG cytosines (CpH). The study also shows that CpH methylation can repress transcription. Furthermore, CpH methylation is recognized by the Rett syndrome–associated protein MeCP2, which is established during neuronal maturation and maintained by DNA methyltransferase DNMT3A. DNA methylation has critical roles in the nervous system and has been traditionally considered to be restricted to CpG dinucleotides in metazoan genomes. Here we show that the single base–resolution DNA methylome from adult mouse dentate neurons consists of both CpG (∼75%) and CpH (∼25%) methylation (H = A/C/T). Neuronal CpH methylation is conserved in human brains, enriched in regions of low CpG density, depleted at protein-DNA interaction sites and anticorrelated with gene expression. Functionally, both methylated CpGs (mCpGs) and mCpHs can repress transcription in vitro and are recognized by methyl-CpG binding protein 2 (MeCP2) in neurons in vivo . Unlike most CpG methylation, CpH methylation is established de novo during neuronal maturation and requires DNA methyltransferase 3A (DNMT3A) for active maintenance in postmitotic neurons. These characteristics of CpH methylation suggest that a substantially expanded proportion of the neuronal genome is under cytosine methylation regulation and provide a new foundation for understanding the role of this key epigenetic modification in the nervous system.