Selective penetration of fullerenol through pea seed coats mitigates osmosis-repressed germination via chromatin remodeling and transcriptional reprograming.

BACKGROUND: The alteration of chromatin accessibility plays an important role in plant responses to abiotic stress. Carbon-based nanomaterials (CBNMs) have attracted increasing interest in agriculture due to their potential impact on crop productivity, showcasing effects on plant biological processes at transcriptional levels; however, their impact on chromatin accessibility remains unknown. RESULTS: This study found that fullerenol can penetrate the seed coat of pea to mitigate the reduction of seed germination caused by osmotic stress. RNA sequencing (RNA-seq) revealed that the application of fullerenol caused the high expression of genes related to oxidoreduction to return to a normal level. Assay for transposase accessible chromatin sequencing (ATAC-seq) confirmed that fullerenol application reduced the overall levels of chromatin accessibility of numerous genes, including those related to environmental signaling, transcriptional regulation, and metabolism. CONCLUSION: This study suggests that fullerenol alleviates osmotic stress on various fronts, encompassing antioxidant, transcriptional, and epigenetic levels. This advances knowledge of the working mechanism of this nanomaterial within plant cells. © 2024 Society of Chemical Industry.

Cloning and functional mechanism of the dwarf gene gba affecting stem elongation and cellulose biosynthesis in jute (Corchorus olitorius).

Plant height (PH) is an important factor affecting bast fiber yield in jute. Here, we report the mechanism of dwarfism in the 'Guangbaai' (gba) of jute. The mutant gba had shorter internode length and cell length compared to the standard cultivar 'TaiZi 4' (TZ4). Exogenous GA3 treatment indicated that gba is a GA-insensitive dwarf mutant. Quantitative trait locus (QTL) analysis of three PH-related traits via a high-density genetic linkage map according to re-seq showed that a total of 25 QTLs were identified, including 13 QTLs for PH, with phenotypic variation explained ranging from 2.42 to 74.16%. Notably, the functional mechanism of the candidate gene CoGID1a, the gibberellic acid receptor, of the major locus qPHIL5 was evaluated by transgenic analysis and virus-induced gene silencing. A dwarf phenotype-related single nucleotide mutation in CoGID1a was identified in gba, which was also unique to the dwarf phenotype of gba among 57 cultivars. Cogid1a was unable to interact with the growth-repressor DELLA even in the presence of highly accumulated gibberellins in gba. Differentially expressed genes between transcriptomes of gba and TZ4 after GA3 treatment indicated up-regulation of genes involved in gibberellin and cellulose synthesis in gba. Interestingly, it was found that up-regulation of CoMYB46, a key transcription factor in the secondary cell wall, by the highly accumulated gibberellins in gba promoted the expression of cellulose synthase genes CoCesA4 and CoCesA7. These findings provide valuable insights into fiber development affected by endogenous gibberellin accumulation in plants.

Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus).

BACKGROUND: Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes. RESULTS: In this study, we investigated the satellite repeat signature in five okra (Abelmoschus esculentus) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA. CONCLUSIONS: Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes.

Effects of the combination of Lactobacillus helveticus and isomalto-oligosaccharide on survival, gut microbiota, and immune function in Apis cerana worker bees.

The adult worker bees were fed sucrose syrup or sucrose syrup supplemented with Lactobacillus helveticus KM7, prebiotic isomalto-oligosaccharide (IMO), or L. helveticus KM7 combined with IMO. Survival rate, gut microbiota, and gene expression of gut antimicrobial peptides in worker honey bees were determined. Administration of L. helveticus KM7 and IMO significantly increased the survival rate in worker bees relative to bees fed sucrose only. Then, higher concentration of both lactic acid bacteria and Bifidobacterium in the gut and lower counts of gut fungi, Enterococcus, and Bacteroides-Porphyromonas-Prevotella were observed in bees fed the combination of KM7 and IMO compared with control bees. The combination of L. helveticus KM7 with IMO showed a greater or comparable modulating effect on those bacteria relative to either KM7 or IMO alone. Furthermore, the combination treatment of L. helveticus KM7 and IMO enhanced mRNA expression of antimicrobial peptide genes, including Abaecin, Defensin, and the gene encoding prophenoloxidase (PPO) in the gut compared with both control bees and those either L. helveticus KM7 or IMO alone. These results suggest that the combination of L. helveticus KM7 and IMO synergistically modifies the gut microbiota and immunity and consequently improves the survival rate of Apis cerana adult workers.

Genome-wide association study reveals loci and candidate genes of flowering time in jute (Corchorus L.).

Suitable flowering time can improve fiber yield and quality, which is of great significance for jute biological breeding. In this study, 242 jute accessions were planted in Fujian for 2 consecutive years, and 244,593 SNPs distributed in jute genome were used for genome-wide association analysis of flowering time. A total of 19 candidate intervals (P < 0.0001) were identified by using GLM and FaST-LMM and were significantly associated with flowering time, with phenotypic variation explained (PVE) ranging from 5.8 to 18.61%. Six stable intervals that were repeatedly detected in different environments were further identified by the linkage disequilibrium heatmap. The most likely 7 candidate genes involved to flowering time were further predicted according to the gene functional annotations. Notably, functional analysis of the candidate gene CcPRR7 of the major loci qFT-3-1, a key factor in circadian rhythm in the photoperiodic pathway, was evaluated by linkage, haplotype, and transgenic analysis. ß-glucuronidase (GUS) and luciferase (LUC) activity assay of the promoters with two specific haplotypes confirmed that the flowering time can be controlled by regulating the expression of CcPRR7. The model of CcPRR7 involved in the photoperiod regulation pathway under different photoperiods was proposed. These findings provide insights into genetic loci and genes for molecular marker-assisted selection in jute and valuable information for genetically engineering PRR7 homologs in plants. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01435-8.

Transarterial chemoembolization plus camrelizumab is an effective and tolerable bridging therapy for patients with intermediate­stage hepatocellular carcinoma: A pilot study.

Transarterial chemoembolization (TACE) has been reported to synergize with camrelizumab in the treatment of hepatocellular carcinoma (HCC). The present study aimed to explore the potential of TACE and camrelizumab as a bridging therapy prior to surgery for patients with HCC. For this purpose, 11 patients with HCC with intermediate stage disease [classified by China Liver Cancer (CNLC) staging] who received TACE combined with camrelizumab as a bridging therapy prior to surgery were enrolled in this study. The treatment response was evaluated at 2 weeks following TACE therapy and following camrelizumab treatment. The relapse-free survival (RFS) and overall survival (OS) of the patients were calculated. The objective response and disease control rates were 72.7 and 100.0% following TACE treatment, and were 100.0 and 100.0% following camrelizumab treatment, respectively. The α-fetoprotein levels gradually decreased following TACE, camrelizumab treatment and surgical resection (all P<0.05). Of note, the CNLC stage decreased following treatment (P=0.007) and the downstaging success rate was 63.6%. In terms of survival profiles, the mean RFS (95% CI) was 14.1 (11.7-16.5) months and the 1-year RFS rate was 77.9±14.1%. Furthermore, the mean OS (95% CI) was 15.0 (13.2-16.8) months and the 1-year OS rate was 80.0±17.9%. Successful downstaging was associated with RFS (P=0.041), but not OS (P=0.221). With regard to safety, 6 (54.5%) patients experienced reactive cutaneous capillary endothelial proliferation, 5 (45.5%) patients reported pain and 4 (36.4%) patients had a fever. On the whole, the present study demonstrated that TACE plus camrelizumab may be an effective and safe strategy that has potential for use as a bridging strategy prior to surgery in patients with intermediate-stage HCC.

Adaptation of agriculture to extreme weather events: evidence from apple farmers' organic fertilizer use in China.

Overcoming the challenge of more frequent and extreme weather events holds importance in agricultural production. We take spring frost disasters as a representative extreme weather event to identify how perennial economic crop farmers adjust the quantity of organic fertilizer used in response to extreme weather events and their adjustment mechanism. In this study, we establish a conceptual framework for the adaptation mechanism of apple growers under extreme weather events. This article draws and verifies five hypotheses through on-site investigations of apple growers in Shaanxi Province, China. Empirical evidence shows that farmers increase the quantity of commercial organic fertilizer materials in the year and in the following year when spring frost occurs, indicating that their adaptative behavior can be subdivided into repair and prevention. Mechanism analysis shows that liquidity constraints impact farmers' adaptive behavior. Liquidity constraints limit the ability of farmers to increase the quantity of commercial organic fertilizer materials to adapt to a spring frost disaster. Furthermore, for farmers not constrained by liquidity constraints, household resource endowment conditions still affect their adaptive behavior. Significantly, the household labor force size mainly influences farmers to increase commercial organic fertilizer to adapt to a spring frost disaster. Our findings highlight the differences between the adaptive behavior mechanism of perennial crop farmers and food crop farmers. Moreover, we reconfirm the stimulating effect of organic fertilizer on crop production.

Genome-wide analysis of the SMXL gene family in common bean and identification of karrikin-responsive PvSMXL2 as a negative regulator of PEG-induced drought stress.

Common bean (Phaseolus vulgaris L.) is a major legume crop worldwide, but its growth and development frequently face challenges due to abiotic stresses, particularly drought. Proper supplement of copper could mitigate the adverse effects of drought, but excessive accumulation of this metal in plants can be harmful. The suppressor of MAX2 1-like (SMXL) gene family, which plays important roles in various plant processes, including stress responses, remains poorly understood in common bean. In this study, we identified nine orthologues of SMXL genes in common bean, which are located on six chromosomes and classified into four subgroups. Basic molecular properties, including theoretical isoelectric point (PI), molecular weight (MW), grand average of hydropathicity (GVIO), gene structure, and conserved motifs were characterized, and numerous cis-elements in promoters were predicted. The expression patterns of PvSMXL genes were found to be distinct under 10% polyethylene glycol (PEG)-induced drought stress and 200 µM Cu treatments. Most PvSMXLs showed reduced expression in response to Cu treatment, whereas nearly half PvSMXLs exhibited inducible expression under drought stress. PvSMXL2, which exhibited a rapid response to karrikin 1 (KAR1), an active form of the plant growth regulators newly found in the smoke of burning plant material, was down-regulated by both PEG-induced drought and Cu stresses. Transient silencing of PvSMXL2 resulted in enhanced drought stress tolerance without conferring Cu tolerance. These findings provide valuable insights into the functions of SMXL genes in common bean under abiotic stress conditions.

Comprehensive analysis of m6A regulators characterized by the immune microenvironment in Duchenne muscular dystrophy.

BACKGROUND: Duchenne muscular dystrophy (DMD) is an X-linked, incurable, degenerative neuromuscular disease that is exacerbated by secondary inflammation. N6-methyladenosine (m6A), the most common base modification of RNA, has pleiotropic immunomodulatory effects in many diseases. However, the role of m6A modification in the immune microenvironment of DMD remains elusive. METHODS: Our study retrospectively analyzed the expression data of 56 muscle tissues from DMD patients and 26 from non-muscular dystrophy individuals. Based on single sample gene set enrichment analysis, immune cells infiltration was identified and the result was validated by flow cytometry analysis and immunohistochemical staining. Then, we described the features of genetic variation in 26 m6A regulators and explored their relationship with the immune mircoenvironment of DMD patients through a series of bioinformatical analysis. At last, we determined subtypes of DMD patients by unsupervised clustering analysis and characterized the molecular and immune characteristics in different subgroups. RESULTS: DMD patients have a sophisticated immune microenvironment that is significantly different from non-DMD controls. Numerous m6A regulators were aberrantly expressed in the muscle tissues of DMD and inversely related to most muscle-infiltrating immune cell types and immune response-related signaling pathways. A diagnostic model involving seven m6A regulators was established using LASSO. Furthermore, we determined three m6A modification patterns (cluster A/B/C) with distinct immune microenvironmental characteristics. CONCLUSION: In summary, our study demonstrated that m6A regulators are intimately linked to the immune microenvironment of muscle tissues in DMD. These findings may facilitate a better understanding of the immunomodulatory mechanisms in DMD and provide novel strategies for the treatment.

Highly Sensitive and Selective Detection of Pharmaceuticals on Au/MIL-101(Cr) by SERS.

The detection of pharmaceuticals has been a matter of concern among scientists and health researchers in the past few decades. However, it is still difficult to realize the sensitivity and selectivity detection of pharmaceuticals with similar structures. Herein, the pharmaceutical molecules of 2-mercaptobenzimidazole (MBI) and 2-mercaptobenzothiazole (MBT) with so similar structures can be selectively detected by surface-enhanced Raman spectroscopy (SERS) taking advantage of the fingerprint identification on Au/MIL-101(Cr), with sensitive detection limits of 0.5 ng·mL-1 for MBI and 1 ng·mL-1 for MBT. MBI is selectively enriched by Au/MIL-101(Cr) from the mixture solution and detected by SERS below 30 ng·mL-1. MBI can also be selectively detected in the serum samples with a detection limit of 10 ng·mL-1. Density functional theory calculations combined with the SERS experiments explained that the high sensitivity and selectivity are caused by the intrinsic differences in Raman intensity and different adsorption energies from the pharmaceutical molecules adsorbed on Au/MIL-101(Cr), respectively. This study provides an effective way to enrich and detect pharmaceutical molecules with similar structures.

CDK12 and Integrator-PP2A complex modulates LEO1 phosphorylation for processive transcription elongation.

Cyclin-dependent kinase 12 (CDK12) interacts with cyclin K to form a functional nuclear kinase that promotes processive transcription elongation through phosphorylation of the C-terminal domain of RNA polymerase II (Pol II). To gain a comprehensive understanding of CDK12's cellular function, we used chemical genetic and phosphoproteomic screening to identify a landscape of nuclear human CDK12 substrates, including regulators of transcription, chromatin organization, and RNA splicing. We further validated LEO1, a subunit of the polymerase-associated factor 1 complex (PAF1C), as a bona fide cellular substrate of CDK12. Acute depletion of LEO1, or substituting LEO1 phosphorylation sites with alanine, attenuated PAF1C association with elongating Pol II and impaired processive transcription elongation. Moreover, we discovered that LEO1 interacts with and is dephosphorylated by the Integrator-PP2A complex (INTAC) and that INTAC depletion promotes the association of PAF1C with Pol II. Together, this study reveals an uncharacterized role for CDK12 and INTAC in regulating LEO1 phosphorylation, providing important insights into gene transcription and its regulation.

Evolution and expression analysis of the caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) gene family in jute (Corchorus L.).

BACKGROUND: Jute is considered one of the most important crops for fiber production and multipurpose usages. Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is a crucial enzyme involved in lignin biosynthesis in plants. The potential functions of CCoAOMT in lignin biosynthesis of jute have been reported in several studies. However, little is known about the evolution of the CCoAOMT gene family, and either their expression level at different developing stages in different jute cultivars, as well as under abiotic stresses including salt and drought stress. RESULTS: In the present study, 66 CCoAOMT genes from 12 species including 12 and eight CCoAOMTs in Corchorus olitorius and C. capsularis were identified. Phylogenetic analysis revealed that CCoAOMTs could be divided into six groups, and gene expansion was observed in C. olitorius. Furthermore, gene expression analysis of developing jute fibers was conducted at different developmental stages (15, 30, 45, 60, and 90 days after sowing [DAS]) in six varieties (Jute-179 [J179], Lubinyuanguo [LB], and Qiongyueqing [QY] for C. capsularis; Funong No.5 [F5], Kuanyechangguo [KY], and Cvlv [CL] for C. olitorius). The results showed that CCoAOMT1 and CCoAOMT2 were the dominant genes in the CCoAOMT family. Of these two dominant CCoAOMTs, CCoAOMT2 showed a constitutive expression level during the entire growth stages, while CCoAOMT1 exhibited differential expression patterns. These two genes showed higher expression levels in C. olitorius than in C. capsularis. The correlation between lignin content and CCoAOMT gene expression levels indicated that this gene family influences the lignin content of jute. Using real-time quantitative reverse transcription PCR (qRT-PCR), a substantial up-regulation of CCoAOMTs was detected in stem tissues of jute 24 h after drought treatment, with an up to 17-fold increase in expression compared to that of untreated plants. CONCLUSIONS: This study provides a basis for comprehensive genomic studies of the entire CCoAOMT gene family in C. capsularis and C. olitorius. Comparative genomics analysis among the CCoAOMT gene families of 12 species revealed the close evolutionary relationship among Corchorus, Theobroma cacao and Gossypium raimondii. This study also shows that CCoAOMTs are not only involved in lignin biosynthesis, but also are associated with the abiotic stress response in jute, and suggests the potential use of these lignin-related genes to genetically improve the fiber quality of jute.

OBHS Drives Abnormal Glycometabolis Reprogramming via GLUT1 in Breast Cancer.

Due to the poor metabolic conditions fomenting the emergence of the Warburg effect (WE) phenotype, abnormal glycometabolism has become a unique and fundamental research topic in the field of tumor biology. Moreover, hyperglycemia and hyperinsulinism are associated with poor outcomes in patients with breast cancer. However, there are a few studies on anticancer drugs targeting glycometabolism in breast cancer. We hypothesized that Oxabicycloheptene sulfonate (OBHS), a class of compounds that function as selective estrogen receptor modulators, may hold potential in a therapy for breast cancer glycometabolism. Here, we evaluated concentrations of glucose, glucose transporters, lactate, 40 metabolic intermediates, and glycolytic enzymes using an enzyme-linked immunosorbent assay, Western blotting, and targeted metabolomic analysis in, in vitro and in vivo breast cancer models. OBHS significantly inhibited the expression of glucose transporter 1 (GLUT1) via PI3K/Akt signaling pathway to suppress breast cancer progression and proliferation. Following an investigation of the modulatory effect of OBHS on breast cancer cells, we found that OBHS suppressed the glucose phosphorylation and oxidative phosphorylation of glycolytic enzymes, leading to the decreased biological synthesis of ATP. This study was novel in highlighting the role of OBHS in the remodeling of tumor glycometabolism in breast cancer, and this is worth further investigation of breast cancer in clinical trials.

Understanding water conservation vs. profligation traits in vegetable legumes through a physio-transcriptomic-functional approach.

Vegetable soybean and cowpea are related warm-season legumes showing contrasting leaf water use behaviors under similar root drought stresses, whose mechanisms are not well understood. Here we conducted an integrative phenomic-transcriptomic study on the two crops grown in a feedback irrigation system that enabled precise control of soil water contents. Continuous transpiration rate monitoring demonstrated that cowpea used water more conservatively under earlier soil drought stages, but tended to maintain higher transpiration under prolonged drought. Interestingly, we observed a soybean-specific transpiration rate increase accompanied by phase shift under moderate soil drought. Time-series transcriptomic analysis suggested a dehydration avoidance mechanism of cowpea at early soil drought stage, in which the VuHAI3 and VuTIP2;3 genes were suggested to be involved. Multifactorial gene clustering analysis revealed different responsiveness of genes to drought, time of day and their interactions between the two crops, which involved species-dependent regulation of the circadian clock genes. Gene network analysis identified two co-expression modules each associated with transpiration rate in cowpea and soybean, including a pair of negatively correlated modules between species. Module hub genes, including the ABA-degrading gene GmCYP707A4 and the trehalose-phosphatase/synthase gene VuTPS9 were identified. Inter-modular network analysis revealed putative co-players of the hub genes. Transgenic analyses verified the role of VuTPS9 in regulating transpiration rate under osmotic stresses. These findings propose that species-specific transcriptomic reprograming in leaves of the two crops suffering similar soil drought was not only a result of the different drought resistance level, but a cause of it.

Identification of AREB/ABF Gene Family Involved in the Response of ABA under Salt and Drought Stresses in Jute (Corchorus olitorius L.).

The abscisic acid (ABA)-responsive element binding protein/ABRE-binding factor (AREB/ABF) subfamily members are essential to ABA signaling pathways and plant adaptation to various environmental stresses. Nevertheless, there are no reports on AREB/ABF in jute (Corchorus L.). Here, eight AREB/ABF genes were identified in the C. olitorius genome and classified into four groups (A-D) based on their phylogenetic relationships. A cis-elements analysis showed that CoABFs were widely involved in hormone response elements, followed by light and stress responses. Furthermore, the ABRE response element was involved in four CoABFs, playing an essential role in the ABA reaction. A genetic evolutionary analysis indicated that clear purification selection affects jute CoABFs and demonstrated that the divergence time was more ancient in cotton than in cacao. A quantitative real-time PCR revealed that the expression levels of CoABFs were upregulated and downregulated under ABA treatment, indicating that CoABF3 and CoABF7 are positively correlated with ABA concentration. Moreover, CoABF3 and CoABF7 were significantly upregulated in response to salt and drought stress, especially with the application of exogenous ABA, which showed higher intensities. These findings provide a complete analysis of the jute AREB/ABF gene family, which could be valuable for creating novel jute germplasms with a high resistance to abiotic stresses.

Model construction of factors influencing intensive care unit nurses' medical device-related pressure injury knowledge, attitude, and practice.

The ability of knowledge, attitude, and practice of intensive care unit (ICU) nurses to perform medical device-related pressure injuries (MDRPIs) can affect the incidence of MDRPI in ICU patients. Therefore, in order to improve ICU nurses' understanding and nursing ability of MDRPIs, we investigated the non-linear relationship (synergistic and superimposed relationships) between the factors influencing ICU nurses' ability of knowledge, attitude, and practice. A Clinical Nurses' Knowledge, Attitude, and Practice Questionnaire for the Prevention of MDRPI in Critically Ill Patients was administered to 322 ICU nurses from tertiary hospitals in China from January 1, 2022 to June 31, 2022. After the questionnaire was distributed, the data were collected and sorted out, and the corresponding statistical analysis and modelling software was used to analyse the data. IBM SPSS 25.0 software was used to conduct Single factor analysis and Logistic regression analysis on the data, so as to screen the statistically significant influencing factors. IBM SPSS Modeler18.0 software was used to construct a decision tree model of the factors influencing MDRPI knowledge, attitude, and practice of ICU nurses, and ROC curves were plotted to analyse the accuracy of the model. The results showed that the overall passing rate of ICU nurses' knowledge, attitude, and practice score was 72%. The statistically significant predictor variables ranked in importance were education background (0.35), training (0.31), years of working (0.24), and professional title (0.10). AUC = 0.718, model prediction performance is good. There is a synergistic and superimposed relationship between high education background, attended training, high years of working and high professional title. Nurses with the above factors have strong MDRPI knowledge, attitude, and practice ability. Therefore, nursing managers can develop a reasonable and effective scheduling system and MDRPI training program based on the study results. The ultimate goal is to improve the ability of ICU nurses to know and act on MDRPI and to reduce the incidence of MDRPI in ICU patients.

Transcriptome Dynamics of Common Bean Roots Exposed to Various Heavy Metals Reveal Valuable Target Genes and Promoters for Genetic Engineering.

Understanding the gene regulatory basis of plant response to heavy metals (HMs) is fundamental for the management of food safety and security. However, a comprehensive and comparative view of the plant responses to different HMs is still lacking. Here, we compared root transcriptomes in common bean under 9 HM treatments at 50 µM for three time points each. Cd, Cr, Co, Ni, and Pb caused most severe morphological and/or biochemical retardations. A total of 448 genes were found to be responsive to all nine HMs, which were mostly involved in photosynthesis, oxidization-reduction, and ion binding. Cd and Cu triggered the greatest number of unique differentially expressed genes (DEG)s, which were predominantly related to cellular transport/localization in the former and RNA binding in the latter. Short-term and prolonged HM treatments shaped very different DEG patterns. Weighted gene co-expression network analysis identified six co-expression modules showing exceptionally high transcripts abundance in specific HM × time scenarios. We experimentally verified the promoter activity of the gene GIP1 and the novel function of XTH23 under Cu/Cd stress. Collectively, the transcriptomic atlas provides valuable resources for better understanding the common and unique mechanisms of plant response to different HMs and offers a mass of candidate target genes/promoters for genetic engineering.

G-quadruplexes sense natural porphyrin metabolites for regulation of gene transcription and chromatin landscapes.

BACKGROUND: G-quadruplexes (G4s) are unique noncanonical nucleic acid secondary structures, which have been proposed to physically interact with transcription factors and chromatin remodelers to regulate cell type-specific transcriptome and shape chromatin landscapes. RESULTS: Based on the direct interaction between G4 and natural porphyrins, we establish genome-wide approaches to profile where the iron-liganded porphyrin hemin can bind in the chromatin. Hemin promotes genome-wide G4 formation, impairs transcription initiation, and alters chromatin landscapes, including decreased H3K27ac and H3K4me3 modifications at promoters. Interestingly, G4 status is not involved in the canonical hemin-BACH1-NRF2-mediated enhancer activation process, highlighting an unprecedented G4-dependent mechanism for metabolic regulation of transcription. Furthermore, hemin treatment induces specific gene expression profiles in hepatocytes, underscoring the in vivo potential for metabolic control of gene transcription by porphyrins. CONCLUSIONS: These studies demonstrate that G4 functions as a sensor for natural porphyrin metabolites in cells, revealing a G4-dependent mechanism for metabolic regulation of gene transcription and chromatin landscapes, which will deepen our knowledge of G4 biology and the contribution of cellular metabolites to gene regulation.