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Histone 3 Lys 27 trimethylation (H3K27me3)-mediated epigenetic silencing plays a critical role in multiple biological processes. However, the H3K27me3 recognition and transcriptional repression mechanisms are only partially understood. Here, we report a mechanism for H3K27me3 recognition and transcriptional repression. Our structural and biochemical data showed that the BAH domain protein AIPP3 and the PHD proteins AIPP2 and PAIPP2 cooperate to read H3K27me3 and unmodified H3K4 histone marks, respectively, in Arabidopsis . The BAH-PHD bivalent histone reader complex silences a substantial subset of H3K27me3-enriched loci, including a number of development and stress response-related genes such as the RNA silencing effector gene ARGONAUTE 5 ( AGO5 ). We found that the BAH-PHD module associates with CPL2, a plant-specific Pol II carboxyl terminal domain (CTD) phosphatase, to form the BAH-PHD-CPL2 complex (BPC) for transcriptional repression. The BPC complex represses transcription through CPL2-mediated CTD dephosphorylation, thereby causing inhibition of Pol II release from the transcriptional start site. Our work reveals a mechanism coupling H3K27me3 recognition with transcriptional repression through the alteration of Pol II phosphorylation states, thereby contributing to our understanding of the mechanism of H3K27me3-dependent silencing. Histone 3 Lys 27 trimethylation (H3K27me3) mediates epigenetic silencing of gene expression. Here, Zhang et al. show that in Arabidopsis, the BAH-domain H3K27me3-reader protein AIPP3 forms a complex with PHD proteins and CPL2, a plant-specific Pol II phosphatase, to inhibit Pol II activity by dephosphorylation.

Mammalian SWI/SNF complex is a key chromatin remodeler that reshapes nucleosomes and regulates DNA accessibility. Mutations in SWI/SNF subunits are found in a broad spectrum of human cancers; however, the mechanisms of how these aberrations of SWI/SNF complex would impact tumorigenesis and cancer therapeutics remain to be elucidated. Studies have demonstrated that immune checkpoint blockade (ICB) therapy is promising in cancer treatment. Nevertheless, suitable biomarkers that reliably predict the clinical response to ICB are still lacking. Emerging evidence has suggested that SWI/SNF components play novel roles in the regulation of anti-tumor immunity, and SWI/SNF deficiency can be therapeutically targeted by ICB. These findings manifest the prominence of the SWI/SNF complex as a stratification biomarker that predicts treatment (therapeutic) response to ICB. In this review, we summarize the recent advances in ICB therapy by harnessing the cancer-specific vulnerability elicited by SWI/SNF deficiency. We provide novel insights into a comprehensive understanding of the underlying mechanisms by which SWI/SNF functions as a modulator of anti-tumor immunity.

Benzo(a)pyrene (BaP), the earliest and most significant carcinogen among polycyclic aromatic hydrocarbons (PAHs), has been found in foods, tobacco smoke, and automobiles exhaust, etc. Exposure to BaP induced DNA damage directly, or oxidative stress-related damage, resulting in cell apoptosis and carcinogenesis in human respiratory system, digestive system, reproductive system, etc. Moreover, BaP triggered genome-wide epigenetic alterations by methylation, which might cause disturbances in regulation of gene expression, and thereby induced cancer. It has been proved that BaP reduced genome-wide DNA methylation, and activated proto-oncogene by hypomethylation in the promoter region, but silenced tumor suppressor genes by promoter hypermethylation, resulting in cancer initiation and progression. Here we summarized the changes in DNA methylation in BaP exposure, and revealed the methylation of DNA plays a role in cancer development. Graphical Abstract

A new automatic method for dispersion curve picking based on Hessian matrix attributes is proposed, on which, an algorithm is developed in this paper. The algorithm is based on dispersion power spectra transformed from surface waves. It fulfills the automatic picking of the surface wave dispersion curves from the fundamental to high orders, by ridge searching and extraction, ridge line segment connection, dispersion curve selecting and order sorting. The algorithm does not have to rely on model training and there is no manual interaction requirement. This inherent efficiency advantage of the algorithm provides an efficient tool for surface wave dispersion curve picking for large projects such as oil and gas exploration. The algorithm is tested using two conceptual models. On the synthetic data of the test models, surface wave dispersion curves up to the 8th order are successfully picked, which shows the excellent picking ability of the method. Further comparative experiments show that the algorithm is superior to other methods in terms of picking accuracy, completeness, anti-noise performance and computation efficiency. In order to evaluate the practicability of the algorithm, we applied it to surface wave data from an industrial prospecting project. Three dispersion curves, including the fundamental order, first order and second order, are successfully obtained. The dispersion curve inversion result matches perfectly with the vertical seismic profile. This application case verified the effectiveness and practicability of the algorithm.

Potato tubers undergo greening and accumulate steroidal glycoalkaloids (SGAs) upon light exposure, posing potential food safety risks. In this study, six potato cultivars (“Favorita”, “Lucinda”, “Jizhangshu 12”, “Longshu 10”, “Qingshu 9”, and “Purple Potato”) were subjected to six light treatments (dark, UVA, blue, green, red, and white), and peel color, pigment content, SGAs, and the expression of genes related to light signaling, chlorophyll biosynthesis, and SGA biosynthesis was evaluated. Under green light, the contents of α-solanine and α-chaconine were 76.22 and 171.84 mg/kg fresh weight (FW), respectively; by contrast, their levels under blue and white light were approximately 60% higher. These effects may be mediated by the upregulation of HY5 and COP1 expression, which in turn could regulate the biosynthesis of chlorophyll-related genes (CHID, CHLI1) and SGA-related genes (HMGR, SGT1). Yellow-skinned cultivars exhibited pronounced light sensitivity (chlorophyll 18.47–18.52 mg/kg FW; SGAs up to 290.41 mg/kg FW), whereas red- and purple-skinned cultivars delayed greening through anthocyanin-mediated light attenuation. Collectively, these findings provide a framework for postharvest management and breeding, suggesting that reducing blue light while enhancing green light in spectral illumination, together with the development of anthocyanin-enriched cultivars, may serve as effective strategies to extend shelf life, mitigate food safety risks, and reduce postharvest losses.

Enzymatic browning markedly reduces the processing quality and economic value of potatoes. This study evaluated the effects of copper sulfate (CuSO4) on potato growth, yield, and enzymatic browning. Quantitative analysis of browning-related enzymes, organic acids, free amino acids, and the browning index (BI) was conducted using high-performance liquid chromatography and non-contact colorimetric technology. Moderate Cu2+ (0.078–0.157 mmol·L−1) supply enhanced photosynthetic capacity, biomass, and starch accumulation, whereas excessive Cu induced oxidative stress, increased PPO activity, phenolic accumulation, and BI. Metabolic profiling revealed that Cu2+ activates PPO via its copper-binding sites and reprograms amino acid and organic acid metabolism—upregulating arginine and proline while downregulating isoleucine, leucine, phenylalanine, lysine, citrate, and chlorogenic acid, all strongly correlated with BI. These findings highlight the dual role of copper in yield formation and enzymatic browning, introducing metabolic reprogramming as a potential mechanism for optimizing Cu fertilization to balance productivity and postharvest quality.

Background As a multi-use cash crop, the yield and quality traits of potatoes are often affected by genotype × environment interactions (GEI). Understanding the influence of GEI on potato yield and quality across varying environmental conditions is crucial for selecting excellent varieties suitable for specific ecological regions. Methods Ten advanced potato lines and twenty-two cultivars were assessed at three pilot sites in Gansu Province, China over two successive years (2020–2021). Tuber yield, dry matter, starch, reducing sugar, carotenoid, vitamin C, pyridoxamine, thiamine, nicotinic acid, pyridoxal and pyridoxine were analyzed. Results An analysis of variance (ANOVA) showed significant effects of GEI on all traits, with the greatest effects observed for vitamin C, reducing sugars, and carotenoids. AMMI, the additive main effects and multiplicative interaction (AMMI), and the genotype main effect plus genotype × environment interaction (GGE) biplot analysis revealed that G25 exhibited high yield, high dry matter content, and high carotenoid content in Weiyuan County. In Anding District, G18 showed high yield, high thiamine content, and low reducing sugar content. Meanwhile, G7 demonstrated superior performance with high yield, high carotenoid and thiamine contents, along with high pyridoxine content in Yongchang County. Genotype recommendations based on the mean values and stability of a single trait are partial and prejudiced, while selections based on multiple traits are desirable. Five ideal genotypes (G23, G26, G25, G24, and G16) were selected by multi-trait stability index (MTSI) in consideration of both the mean values and stability of yield and key quality traits. Conclusions Multi-environment trials revealed that GEI significantly affected vitamin C, reducing sugars, and carotenoids in potato. Five high-yielding and high-quality potato genotypes adapted to different ecological regions of Gansu Province were identified using MTSI analysis. This study provides references for the regional cultivation and quality breeding of potatoes.

Background Steroidal glycoalkaloids (SGAs), derived from cholesterol, act as natural defenses against pathogens and pests. In cultivated potatoes, α-solanine and α-chaconine are the primary SGAs, distributed throughout the plant, with their biosynthesis mechanisms differing across various tissues. The variation in SGAs content between the cortex and perimedullary zone reflects tissue-specific metabolic regulation in potato tuber. Higher SGAs levels in the cortex may enhance defense against external threats. This spatial distribution provides a theoretical basis for breeding strategies aimed at balancing resistance and food quality by regulating SGAs accumulation in specific tissues of potato tubers. Excessive levels of SGAs in potato tubers can compromise both their quality and edibility. Additionally, SGAs exhibit pharmacological properties, including anti-protozoal, antibacterial, antiviral, anti-tumor, and anti-inflammatory effects. Results This study conducted genome-wide association study (GWAS) on SGAs content in the cortex and perimedullary zone of 117 diverse potato germplasm accessions, utilizing 22,983,689 high-quality SNPs. Candidate genes were subjected to analyses of stability, pleiotropy, GO and KEGG enrichment, and haplotype profiling. Twelve candidate genes associated with SGAs biosynthesis in potato tubers were identified, encoding UDP-glycosyltransferase superfamily proteins ( Soltu.DM.11G005750 , Soltu.DM.11G005760 , Soltu.DM.11G005770 , Soltu.DM.11G005820 ), fatty acid hydroxylase superfamily proteins ( Soltu.DM.01G029600 , Soltu.DM.01G029610, Soltu.DM.01G029620 , Soltu.DM.01G029640 , Soltu.DM.01G029650 , Soltu.DM.10G008360 ), alkaline/neutral invertase ( Soltu.DM.11G006090 ), and pleiotropic drug resistance ( Soltu.DM.11G006080 ). Conclusions This study provides a theoretical basis for elucidating the genetic mechanisms underlying SGAs biosynthesis in potatoes and will facilitate the breeding of new potato varieties.

Background Jasmonates (JAs) are one of important phytohormones regulating potato tuber development. It is a complex process and the underlying molecular mechanism regulating tuber development by JAs is still limited. This study attempted to illuminate it through the potential proteomic dynamics information about tuber development in vitro regulated by exogenous JA. Results A combined analysis of physiological and iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic approach was performed in tuber development in vitro under exogenous JA treatments (0, 0.5, 5 and 50 μΜ). Physiological results indicated that low JA concentration (especially 5 μM) promoted tuber development, whereas higher JA concentration (50 μM) showed inhibition effect. A total of 257 differentially expressed proteins (DEPs) were identified by iTRAQ, which provided a comprehensive overview on the functional protein profile changes of tuber development regulated by JA. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that low JA concentration (especially 5 μM) exhibited the promotion effects on tuber development in various cellular processes. Some cell wall polysaccharide synthesis and cytoskeleton formation-related proteins were up-regulated by JA to promote tuber cell expansion. Some primary carbon metabolism-related enzymes were up-regulated by JA to provide sufficient metabolism intermediates and energy for tuber development. And, a large number of protein biosynthesis, degradation and assembly-related were up-regulated by JA to promote tuber protein biosynthesis and maintain strict protein quality control during tuber development. Conclusions This study is the first to integrate physiological and proteomic data to provide useful information about the JA-signaling response mechanism of potato tuber development in vitro . The results revealed that the levels of a number of proteins involved in various cellular processes were regulated by JA during tuber development. The proposed hypothetical model would explain the interaction of these DEPs that associated with tuber development in vitro regulated by JA.

Deciphering the genetic mechanisms underlying key agronomic and quality traits in potato (Solanum tuberosum L.) is essential for advancing varietal improvement. Phenotypic instability in early clonal generations and inbreeding depression, coupled with the complexity of tetrasomic inheritance, pose significant challenges in constructing mapping populations for the genetic dissection of complex traits. Genome-wide association studies (GWASs) offer an efficient method to establish trait–genome associations by analyzing genetic recombination and mutation events in natural populations. This review systematically examines the application of GWASs in identifying agronomic traits in potato, such as plant architecture, yield components, tuber shape, and resistance to early and late blight and nematodes, as well as quality traits including dry matter, starch, and glycoalkaloid content. Some key chromosomal hotspots identified through GWASs include chromosome 5 associated with tuber yield, starch content, and late blight resistance; chromosome 4 and 10 associations with tuber shape and starch content; chromosomes 1, 9, and 11 associated with plant height, tuber number, glycoalkaloid content, and pest resistance. It elucidates the advantages and limitations of GWASs for genetic loci identification in this autotetraploid crop, providing theoretical insights and a reference framework for the precise localization of key genetic loci and the discovery of underlying genes using GWASs.