AIM:To investigate whether vaccinia-related kinase 1(VRK1)mediates transforming growth factor-beta2(TGF-β2)-caused epithelial-mesenchymal transition(EMT)and inflammatory responses in retinal pigment epithelial(RPE)ce...AIM:To investigate whether vaccinia-related kinase 1(VRK1)mediates transforming growth factor-beta2(TGF-β2)-caused epithelial-mesenchymal transition(EMT)and inflammatory responses in retinal pigment epithelial(RPE)cells through regulating snail family transcriptional repressor 1(SNAI1),and to validate its role in a proliferative vitreoretinopathy(PVR)mouse model.METHODS:Human RPE cell line ARPE-19 cells were treated with TGF-β2 to construct an EMT model.Western blot detected VRK1 level.The effects of VRK1 on SNAI1 expression and biological behavior of ARPE-19 cells were detected by immunofluorescence,ELISA,Transwell,and scratch assay,and the interaction between VRK1 and SNAI1 was confirmed through immunoprecipitation.A PVR mouse model was constructed,and the effects of VRK1 or/and SNAI1 on retinal damage were assessed by pathologic staining.Inflammatory factors and EMT-related proteins were assessed with ELISA and Western blot.RESULTS:VRK1 was upregulated in ARPE-19 cells after TGF-β2 treatment.Overexpression of VRK1 increased cell viability,promoted cell migration and EMT,and the levels of inflammatory factors.Silencing of VRK1 reversed the above indexes.There was a direct interaction between VRK1 and SNAI1,and overexpresssion SNAI1 weakened the impacts of silencing of VRK1.In PVR mice,silencing of VRK1 ameliorated retinal structural damage,decreased proinflammatory factor levels,and suppressed SNAI1 and mesenchymal marker expression.SNAI1 overexpression antagonized the protective effects of silencing VRK1 and exacerbated EMT and inflammatory responses.CONCLUSION:VRK1 plays a key role in retinal structural and inflammatory damage in PVR mice by regulating SNAI1 and mediating TGF-β2-caused EMT and inflammatory responses in RPE cells.展开更多
Objectives:The current treatment options and therapeutic targets for triple-negative breast cancer(TNBC),an aggressive subtype of breast cancer(BrCA),are limited.This study aimed to identify novel biomarkers and trans...Objectives:The current treatment options and therapeutic targets for triple-negative breast cancer(TNBC),an aggressive subtype of breast cancer(BrCA),are limited.This study aimed to identify novel biomarkers and transcriptional regulatory networks(TRN)inherent in TNBC samples.Methods:We analyzed pan-cancer BrCA datasets from The Cancer Genome Atlas(TCGA)to compare triple-positive breast cancer(TPBC)with TNBC.TRN algorithms and virtual inference of protein-enriched regulon(VIPER)were used to identify master regulators and their target genes.Utilizing TNBC cells(MDA-MB-231 and MDA-MB-468),we validated the relationship of nuclear factor erythroid 2-like 3(NFE2L3)and basic helix-loop-helix family member E 40(BHLHE40)by performing a luciferase assay.The expression levels of these targets were measured after transfections with plasmid and siRNA via qRT-PCR and western blots.The effect of these genes on cell proliferation and migration was studied using phenotypic assays.Results:Using computational approaches,we identified NFE2L3 as a master regulator with BHLHE40 as its target gene.NFE2L3 protein binds to the promoter region of BHLHE40 and regulates its transcriptional activity.Additionally,silencing and overexpressing NFE2L3 and BHLHE40 in TNBC cell lines MDA-MB-231 and MDA-MB-468 showed that NFE2L3 directly regulates BHLHE40 at both transcriptional and translational levels.We found that BHLHE40 requires NFE2L3 for cell proliferation and migration in TNBC.Conclusion:These findings underscore the significance of NFE2L3 and BHLHE40 in TNBC,highlighting NFE2L3’s role in regulating the oncogenic activity of BHLHE40 in TNBC cells.展开更多
Background:The regulatory mechanisms governing vasculogenic mimicry(VM)in oral squamous cell carcinoma(OSCC)remain largely undefined.This study aimed to identify critical factors and elucidate the epigenetic mechanism...Background:The regulatory mechanisms governing vasculogenic mimicry(VM)in oral squamous cell carcinoma(OSCC)remain largely undefined.This study aimed to identify critical factors and elucidate the epigenetic mechanisms underlying VM in OSCC.Methods:Bioinformatics analysis was performed utilizing single-cell RNA-seq,bulk RNA-seq,and histone H3 lysine 27 acetylation(H3K27ac)Chromatin Immunoprecipitation(ChIP)-seq data obtained from The Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO)databases.ChIP-qPCR was used to validate the binding of ETS transcription factor ELK4(ELK4)to the dihydrofolate reductase(DHFR)enhancer.In vitro VM formation and invasion of OSCC cells were assessed using Matrigel-based tube formation and Transwell assays,respectively.Results:Elevated expression of VM-related genes predicts unfavorable prognosis in OSCC patients.High-dimensional weighted gene co-expression network analysis(hdWGCNA)identified epithelial subcluster C4 as most strongly associated with VM and metastasis.Three co-expression modules within this subcluster exhibited significant positive correlations with both phenotypic traits.Among the 30 eigengenes from the three modules,DHFR emerged as a key regulator of VM and metastasis.Knockdown or inhibition of DHFR significantly suppressed VM formation and invasion in OSCC cells.Mechanistically,ELK4 activated DHFR transcription through direct binding to its enhancer.DHFR overexpression rescued VM and invasion impairment induced by ELK4 knockdown.Conclusion:DHFR was a pivotal enhancer-regulated gene driving VM and metastasis in OSCC.ELK4 directly binds to DHFR enhancer regions to activate its transcription,thereby promoting these malignant phenotypes.These findings identified the ELK4/DHFR axis as a promising therapeutic target for anti-angiogenic intervention in OSCC.展开更多
Chlorogenic acid(CGA),a potent antioxidant with antimicrobial,antiviral,and metabolic regulatory properties,plays multifunctional roles in apple fruit by enhancing postharvest quality,extending shelf life through oxid...Chlorogenic acid(CGA),a potent antioxidant with antimicrobial,antiviral,and metabolic regulatory properties,plays multifunctional roles in apple fruit by enhancing postharvest quality,extending shelf life through oxidative stress reduction,and inhibiting enzymatic browning to preserve color,flavor,and nutritional integrity.Despite the established role of hydroxycinnamoyl transferase(HCT)as a rate-limiting enzyme in CGA biosynthesis,the specific HCT gene responsible for this process and its regulatory mechanisms remain elusive.To address this knowledge gap,we systematically investigated CGA accumulation dynamics during apple storage and functionally characterized MdHCT6,a candidate gene within the HCT family.We found that the chlorogenic acid content in apple fruit increased significantly during postharvest storage compared with the initial storage.Transcriptome analysis showed that the expression level of MdHCT6 was significantly higher than that of other HCT homologues,which was consistent with the reverse transcription quantitative PCR(RT-qPCR)results.In vitro enzymatic assays demonstrated that MdHCT6 catalyzes the synthesis of chlorogenic acid using shikimic acid and quinic acid as precursors,while genetic evidence confirmed its role as a key positive regulator of chlorogenic acid accumulation in apples.Furthermore,we identified the transcription factor MdMYB93 as a direct upstream activator of MdHCT6,establishing a regulatory cascade that governs CGA production.This work not only deciphers the molecular hierarchy of CGA biosynthesis in apples but also provides actionable targets for genetic improvement of antioxidant capacity and postharvest resilience in apple germplasm.展开更多
Mitochondria are semi-autonomous organelles present in eukaryotic cells,containing their own genome and transcriptional machinery.However,their functions are intricately linked to proteins encoded by the nuclear genom...Mitochondria are semi-autonomous organelles present in eukaryotic cells,containing their own genome and transcriptional machinery.However,their functions are intricately linked to proteins encoded by the nuclear genome.Mitochondrial transcription termination factors(mTERFs)are nucleic acid-binding proteins involved in RNA splicing and transcription termination within plant mitochondria and chloroplasts.Despite their recognized importance,the specific roles of mTERF proteins in maize remain largely unexplored.Here,we clone and functionally characterize the maize mTERF18 gene.Our findings reveal that mTERF18 mutations lead to severely undifferentiated embryos,resulting in abortive phenotypes.Early kernel exhibits abnormal basal endosperm transfer layer and a significant reduction in both starch and protein accumulation in mterf18.We identify the mTERF18 gene through mapping-based cloning and validate this gene through allelic tests.mTERF18 is widely expressed across various maize tissues and encodes a highly conserved mitochondrial protein.Transcriptome data reveal that mTERF18 mutations disrupt transcriptional termination of the nad6 gene,leading to undetectable levels of Nad6 protein and reduced complex I assembly and activity.Furthermore,transmission electron microscopy observation of mterf18 endosperm uncover severe mitochondrial defects.Collectively,these findings highlight the critical role of mTERF18 in mitochondrial gene transcription termination and its pivotal impact on maize kernel development.展开更多
Dear Editor,Post-traumatic stress disorder(PTSD)is a chronic neuropsychiatric disorder triggered by severe traumatic events,characterized by persistent intrusive memories,emotional dysregulation,hyperarousal,and avoid...Dear Editor,Post-traumatic stress disorder(PTSD)is a chronic neuropsychiatric disorder triggered by severe traumatic events,characterized by persistent intrusive memories,emotional dysregulation,hyperarousal,and avoidance behaviors[1,2].PTSD is associated with significant gene expression changes in key brain regions,including the ventral tegmental area(VTA),which may underlie dysregulation of dopaminergic signaling and stress-related behaviors[3].展开更多
Drug repurposing offers a promising alternative to traditional drug development and significantly re-duces costs and timelines by identifying new therapeutic uses for existing drugs.However,the current approaches ofte...Drug repurposing offers a promising alternative to traditional drug development and significantly re-duces costs and timelines by identifying new therapeutic uses for existing drugs.However,the current approaches often rely on limited data sources and simplistic hypotheses,which restrict their ability to capture the multi-faceted nature of biological systems.This study introduces adaptive multi-view learning(AMVL),a novel methodology that integrates chemical-induced transcriptional profiles(CTPs),knowledge graph(KG)embeddings,and large language model(LLM)representations,to enhance drug repurposing predictions.AMVL incorporates an innovative similarity matrix expansion strategy and leverages multi-view learning(MVL),matrix factorization,and ensemble optimization techniques to integrate heterogeneous multi-source data.Comprehensive evaluations on benchmark datasets(Fdata-set,Cdataset,and Ydataset)and the large-scale iDrug dataset demonstrate that AMVL outperforms state-of-the-art(SOTA)methods,achieving superior accuracy in predicting drug-disease associations across multiple metrics.Literature-based validation further confirmed the model's predictive capabilities,with seven out of the top ten predictions corroborated by post-2011 evidence.To promote transparency and reproducibility,all data and codes used in this study were open-sourced,providing resources for pro-cessing CTPs,KG,and LLM-based similarity calculations,along with the complete AMVL algorithm and benchmarking procedures.By unifying diverse data modalities,AMVL offers a robust and scalable so-lution for accelerating drug discovery,fostering advancements in translational medicine and integrating multi-omics data.We aim to inspire further innovations in multi-source data integration and support the development of more precise and efficient strategies for advancing drug discovery and translational medicine.展开更多
Chromatin remodeling and transcriptional reprogramming play critical roles during mammalian meiotic prophase I;however,the precise mechanisms regulating these processes remain poorly understood.Our previous work demon...Chromatin remodeling and transcriptional reprogramming play critical roles during mammalian meiotic prophase I;however,the precise mechanisms regulating these processes remain poorly understood.Our previous work demonstrated that deletion of heat shock factor 5(HSF5),a member of the heat shock factor family,induces meiotic arrest and male infertility.However,the molecular pathways through which HSF5 governs meiotic progression have not yet been fully elucidated.In this study,a comprehensive multi-omics approach was applied to investigate the role of HSF5 in modulating chromatin dynamics and transcriptional reprogramming during pachynema progression.Analysis of ATAC-seq and single-cell RNA sequencing data revealed significant alterations in chromatin accessibility and disruption of the transcriptional regulatory network(TRN)in Hsf5−/−spermatocytes.Additionally,HSF5 deficiency resulted in defective XY body formation and altered histone modifications.Notably,Hsf5−/−spermatocytes also exhibited abnormal spermatoproteasome activity specifically on sex chromosomes,with evidence indicating that HSF5 may form a complex with USP7 in vivo to suppress H2AK119ub on meiotic sex chromosomes.These findings provide new insights into the complex,multifunctional role of HSF5 in regulating key meiotic events and advancing our understanding of its function during pachynema progression.展开更多
BACKGROUND Esophageal cancer(ESCA)poses a significant challenge in oncology because of the limited treatment options and poor prognosis.Therefore,enhancing the therapeutic effects of radiotherapy for ESCA and identify...BACKGROUND Esophageal cancer(ESCA)poses a significant challenge in oncology because of the limited treatment options and poor prognosis.Therefore,enhancing the therapeutic effects of radiotherapy for ESCA and identifying relevant therapeutic targets are crucial for improving both the survival rate and quality of life of patients.AIM To define the role of the transcription factor Snail family transcriptional repressor 1(SNAI1)in ESCA,particularly its regulation of radiosensitivity.METHODS A comprehensive analysis of TCGA data assessed SNAI1 expression in ESCA.Survival curves correlated SNAI1 levels with radiotherapy outcomes.Colony formation assays,flow cytometry,and a xenograft model were used to evaluate tumor radiosensitivity and apoptosis.Western blot validated protein expression,while Chromatin im-munoprecipitation assays examined SNAI1's role in regulating epithelial-mesenchymal transition(EMT).RESULTS SNAI1 expression in ESCA cell lines and clinical specimens emphasizes its central role in this disease.Elevated SNAI1 expression is correlated with unfavorable outcomes in radiotherapy.Downregulation of SNAI1 enhances the sensitivity of ESCA cells to ionizing radiation(IR),resulting in remarkable tumor regression upon IR treatment in vivo.This study underscores the direct involvement of SNAI1 in the regulation of EMT,particularly under IR-induced conditions.Furthermore,inhibiting deacetylation effectively suppresses EMT,suggesting a potential avenue to enhance the response to radiotherapy in ESCA.CONCLUSION This study highlights SNAI1's role in ESCA radiosensitivity,offering prognostic insights and therapeutic strategies to enhance radiotherapy by targeting SNAI1 and modulating EMT processes.展开更多
Northern blot analysis was conducted with mitochondrial RNA from seedling leaves, floral buds, and developing seeds of NCa CMS, maintainer line and fertile F1 using ten mitochondrial genes as probes. The results revea...Northern blot analysis was conducted with mitochondrial RNA from seedling leaves, floral buds, and developing seeds of NCa CMS, maintainer line and fertile F1 using ten mitochondrial genes as probes. The results revealed that 9 out of the 10 mitochondrial genes, except for atp6, showed no difference in different tissues of the corresponding materials of NCα CMS system and that they might be constitutively expressed genes. Eight genes, such as orf139, orf222, atpl, cox1, cox2, cob, rm5S, and rm26S, showed no difference among the three tissues of all the materials detected. So the expression of these eight genes was not regulated by nuclear genes and was not tissue-specific. The transcripts of atp9 were identical among different tissues, but diverse among different materials, indicating that transcription of atp9 was neither controlled by nuclear gene nor tissue-specific. Gene atp6 displayed similar transcripts with the same size among different tissues of all the materials but differed in abundance among tissues of corresponding materials and its expression might be tissue-specific under regulation of nuclear gene. Moreover, three transcripts of orf222 were detected in the floral buds of NCa cms and fertile F1, but no transcript was detected in floral buds of the maintainer line.The transcription of orf139 was similar to that of orf222 but only two transcripts of 0.8 kb and 0.6 kb were produced. The atp9 probe detected a single transcript of 0.6 kb in NCa cms and in maintainer line and an additional transcript of 1.2 kb in fertile F1. The relationship of expression of orf222, orf139, and atp9 with NCa sterility was discussed.展开更多
The peaT1 gene fragment was amplified from pGEM-6p-l-peaT1 by PCR, and recovered target gene was cloned into pLexA vector. After digestion and sequencing, the bait vector pLexA-peaT1 was transformed into yeast strain ...The peaT1 gene fragment was amplified from pGEM-6p-l-peaT1 by PCR, and recovered target gene was cloned into pLexA vector. After digestion and sequencing, the bait vector pLexA-peaT1 was transformed into yeast strain EGY48 [p8op-lacZ] by PEG/LiAC, and the transcriptional activity of bait vector was detected. The results showed that recombinant bait plasmid pLexA-PEMG1 was constructed, for the two bands of recombinant bait plasmid in agarose gel eleetrophoresis were expected after digesting by restriction endonuclease EcoR I and Xho I. Therefore, the recombinant bait plasmid could be used in yeast two-hybrid system to screen a cDNA library.展开更多
Auxins were the first of the major plant hormones and played key roles in plant growth and development.Auxin triggered gene expression through several mechanisms.The canonical textbook model is that auxin binds to TIR...Auxins were the first of the major plant hormones and played key roles in plant growth and development.Auxin triggered gene expression through several mechanisms.The canonical textbook model is that auxin binds to TIR1/AFB receptors and stabilizes their interaction with Aux/IAA repressors,leading to their ubiquitination and degradation,which results in activation of ARFs transcription factors.The recent study published in Nature by JiíFriml and co-authors updated the view on gene expression regulated by auxin.The role of TIR-produced cAMP was confirmed to be the second messenger in transcriptional auxin signaling.The conclusions raised in this Nature article shift the paradigm about the regulation of plant growth and development by auxin to the modulation of cAMP production and its interaction with candidate targets.展开更多
In climacteric fruits,the role of ethylene in promoting ripening process and its molecular regulatory mechanisms have been well elucidated.However,research into ethylene's roles in non-climacteric fruits has only ...In climacteric fruits,the role of ethylene in promoting ripening process and its molecular regulatory mechanisms have been well elucidated.However,research into ethylene's roles in non-climacteric fruits has only advanced in recent years,largely because these fruits produce much less ethylene than climacteric fruits.Consequently,reports on its molecular regulatory involvement are still limited.Grape(Vitis vinifera L.),one of the most economically valuable fruits,is regarded as a classical non-climacteric fruit.In this study,an enzyme participating in the last step of ethylene biosynthesis,VvACO1,has been identified as a key enzyme controlling ethylene release in grape fruits(Vitis vinifera‘Jingyan’and‘Red Balado’)using correlation analysis and enzymatic experiments.The transcriptional regulation of VvACO1 was investigated by integrating multiple methods such as DNA pull-down assays,co-expression analysis,dual luciferase reporting system,yeast one-hybrid assays,and transgenic experiments.Our findings revealed that the upregulation of VvACO1 in grape fruits was primarily caused by the removal of transcriptional inhibition.Remarkably,seven transcription factors(TFs)were identified as inhibitors of VvACO1,including VvHY5 from bZIP family,VvWIP2 from C2H2 family,VvBLH1 from Homeobox family,VvAG1 and VvCMB1 from MADS-box family,VvASIL1 and VvASIL2 from Trihelix family.These seven TFs were located in nuclei and exhibited transcriptional inhibition activity.Notably,VvAG1 and VvASIL2 could inhibit VvACO1 expression when overexpressed in grape leaves.Our findings provided theoretical clues for differences of ethylene release regulation between climacteric and non-climacteric fruits,also the identified seven TFs could be potential targets for grape molecular breeding.展开更多
A polyketide synthase-nonribosomal peptide synthetase gene cluster twn in Talaromyces sp.HDN1820200 was activated by overexpression of the pathway-specific transcriptional factor TwnD.Large-scale fermentation and chem...A polyketide synthase-nonribosomal peptide synthetase gene cluster twn in Talaromyces sp.HDN1820200 was activated by overexpression of the pathway-specific transcriptional factor TwnD.Large-scale fermentation and chemical investigation of the mutant strain HDN1820200/TwnD led to the discovery of one new polyketide-amino acid conjugate,bipolamide C and one new polyketide compound,variotin A.The structures of the new compounds were determined by nuclear magnetic resonance(NMR)analysis,high-resolution electrospray ionization mass spectrometry,feeding experiments,NMR calculation and DP4^(+)analysis.This study revealed that the overexpression of the pathway-specific transcriptional factor represents a promising approach for the discovery of new natural products in fungi within specialized habitat.展开更多
Acer paxii belongs to the evergreen species of Acer,but it exhibits a unique feature of reddish leaves in fall in subtropical regions.Although the association of AP2/ERF transcription factors with color change has bee...Acer paxii belongs to the evergreen species of Acer,but it exhibits a unique feature of reddish leaves in fall in subtropical regions.Although the association of AP2/ERF transcription factors with color change has been well-documented in prior research,molecular investigations focusing on AP2/ERF remain notably lacking in Acer paxii.This research focuses on performing an extensive genome-wide investigation to identify and characterize the AP2/ERF gene family in Acer paxii.As a result,123 ApAP2/ERFs were obtained.Phylogenetic analyses categorized the ApAP2/ERF family members into 15 subfamilies.The evolutionary traits of the ApAP2/ERFs were investigated by analyzing their chromosomal locations,conserved proteinmotifs,and gene duplication events.Moreover,investigating gene promoters revealed their potential involvement in developmental regulation,physiological processes,and stress adaptationmechanisms.Measurements of anthocyanin content revealed a notable increase in red leaves during autumn.Utilizing transcriptome data,transcriptomic profiling revealed that the majority of AP2/ERF genes in Acer paxii displayed significant differential expression between red and green leaves during the color-changing period.Furthermore,through qRT-PCR analysis,it was found that the gene expression levels of ApERF006,ApERF014,ApERF048,ApERF097,and ApERF107 were significantly elevated in red leaves.This indicates their potential participation in leaf pigmentation processes.These findings offer significant insights into the biological significance of ApAP2/ERF transcription factors and lay the groundwork for subsequent investigations into their regulatorymechanisms underlying leaf pigmentation in Acer paxii.展开更多
Defensin,an essential component of plant development,is indispensable in pathogen resistance.However,the molecular function of defensins under pathological conditions of Cytospora canker has not been characterized in ...Defensin,an essential component of plant development,is indispensable in pathogen resistance.However,the molecular function of defensins under pathological conditions of Cytospora canker has not been characterized in apple plants.The present study exhibits a detailed overview of the phylogeny and structure of 29 defensins(MdDEF)in apple.Expression analysis revealed that MdDEF genes were spatiotemporally diverse across apple tissues.Five MdDEF genes were found to be significantly up-regulated following a challenge with Cytospora mali.The transgenic overexpression of five defensin genes in apple calli enhanced resistance to C.mali.Among them,MdDEF30 was strongly induced and conferred the highest resistance level in vivo.Meanwhile,antifungal activity assays in vitro demonstrated that a recombinant protein produced from MdDEF30could inhibit the growth of C.mali.Notably,MdDEF30 promoted the accumulation of reactive oxygen species(ROS)and activated defense-related genes such as PR4,PR10,CML13,and MPK3.Co-expression regulatory network analysis showed that MdWRKY75 may regulate the expression of MdDEF30.Further yeast onehybrid(Y1H),luciferase,and chromatin Immunoprecipitation quantitative polymerase chain reaction(ChIPqPCR)assays verified that MdWRKY75 could directly bind to the promoter of MdDEF30.Importantly,pathogen inoculation assays confirmed that MdWRKY75 positively regulates resistance by transcriptionally activating MdDEF30.Overall,these results demonstrated that MdDEF30 promotes resistance to C.mali in apple plants and that MdWRKY75 regulates MdDEF30 expression during the induction of resistance,thereby clarifying biochemical mechanisms of resistance to C.mali in apple trees.展开更多
Since transgene silencing was found in transgenic plants,many scholars have studied it extensively and considered that it has three functional mechanisms:post dependent gene silencing,transcriptional gene silencing,p...Since transgene silencing was found in transgenic plants,many scholars have studied it extensively and considered that it has three functional mechanisms:post dependent gene silencing,transcriptional gene silencing,post transcriptional gene silencing.At the moment,people have mainly focused on the study of post transcriptional gene silencing and found its features:extensivity,conduction and peculiarity,also put forward some hypothesis for its mechanisms,for example,RNA threshold model,aberrant RNA model,inter or intra molecular base pairing model and so on.Furthermore,post transcriptional gene silencing is being applied in gene engineering of plants.Recently the people have found that post transcriptional gene silencing has bearing on capacity plants resisting virus.Many researchers have studied post transcriptional gene silencing,but there are some questions which need be solved in the future.This article summarizes progresses in features,mechanisms,applies of post transcriptional gene silencing about transgenic plants.展开更多
While human immunodeficiency virus 1(HIV-1) infectionis controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from th...While human immunodeficiency virus 1(HIV-1) infectionis controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from the body. Despite decades of research there is still no effective vaccine to prevent HIV-1 infection. Therefore, the possibility of an RNA interference(RNAi)-based cure has become an increasingly explored approach. Endogenous gene expression is controlled at both, transcriptional and post-transcriptional levels by noncoding RNAs, which act through diverse molecular mechanisms including RNAi. RNAi has the potential to control the turning on/off of specific genes through transcriptional gene silencing(TGS), as well as finetuning their expression through post-transcriptional gene silencing(PTGS). In this review we will describe in detail the canonical RNAi pathways for PTGS and TGS, the relationship of TGS with other silencing mechanisms and will discuss a variety of approaches developed to suppress HIV-1 via manipulation of RNAi. We will briefly compare RNAi strategies against other approaches developed to target the virus, highlighting their potential to overcome the major obstacle to finding a cure, which is the specific targeting of the HIV-1 reservoir within latently infected cells.展开更多
As part of our efforts to identify novel contraceptive targets in the epididymis we performed transcriptional profiling on each of the 10 and 19 segments of the mouse and rat epididymidis, respectively, using Affymetr...As part of our efforts to identify novel contraceptive targets in the epididymis we performed transcriptional profiling on each of the 10 and 19 segments of the mouse and rat epididymidis, respectively, using Affymetrix whole genome microarrays. A total of 17 096 and 16 360 probe sets representing transcripts were identified as being expressed in the segmented mouse and rat epididymal transcriptomes, respectively. Comparison of the expressed murine transcripts against a mouse transcriptional profiling database derived from 22 other mouse tissues identified 77 transcripts that were expressed uniquely in the epididymis. The expression of these genes was further evaluated by reverse transcription polymerase chain reaction （RT-PCR） analysis of RNA from 21 mouse tissues. RT-PCR analysis confirmed epididymis-specific expression of Defensin Beta 13 and identified two additional genes with expression restricted only to the epididymis and testis. Comparison of the 16 360 expressed transcripts in the rat epididymis with data of 21 other tissues from a rat transcriptional profiling database identified 110 transcripts specific for the epididymis. Sixty-two of these transcripts were further investigated by qPCR analysis. Only Defensin 22 （E3 epididymal protein） was shown to be completely specific for the epididymis. In addition, 14 transcripts showed more than 100-fold selective expression in the epididymis. The products of these genes might play important roles in epididymal and/or sperm function and further investigation and validation as contraceptive targets are warranted. The results of the studies described in this report are available at the Mammalian Reproductive Genetics （MRG） Database （http：//mrg. genetics.washington.edu/）. （Asian J Androl 2007July; 9： 522-527）展开更多
Retrotransposons account for a large proportion of the genome and genomic variation, and play key roles in creating novel genes and diversifying the genome in many eukaryotic species. Although retrotransposons are abu...Retrotransposons account for a large proportion of the genome and genomic variation, and play key roles in creating novel genes and diversifying the genome in many eukaryotic species. Although retrotransposons are abundant in plants, their roles had been underestimated because of a lack of research. Here, we characterized a gibberellin Acid (GA)-insensitive dwarf mutant, 84133, in foxtail millet. Map-based cloning revealed a 5.5-kb Copia-like retrotransposon insertion in DWARF1 (D1), which encodes a DELLA protein. Transcriptional analysis showed that the Copia retrotransposon mediated the transcriptional reprogramming of D1 leading to a novel N-terminal-deleted truncated DELLA transcript that was putatively driven by Copia's LTR, namely D1-TT, and another chimeric transcript. The presence of D1-TT was confirmed by protein immunodetection analysis. Furthermore, D1-TT protein was resistant to GA3 treatment compared with the intact DELLA protein due to its inability to interact with the GA receptor, SiGID1. Overexpression of D1-TT in foxtail millet resulted in dwarf plants, confirming that it determines the dwarfism of 84133. Thus, our study documents a rare instance of long terminal repeat (LTR) retrotransposon-mediated transcriptional reprograming in the plant kingdom. These results shed light on the function of LTR retrotransposons in generating new gene functions and genetic diversity.展开更多
文摘AIM:To investigate whether vaccinia-related kinase 1(VRK1)mediates transforming growth factor-beta2(TGF-β2)-caused epithelial-mesenchymal transition(EMT)and inflammatory responses in retinal pigment epithelial(RPE)cells through regulating snail family transcriptional repressor 1(SNAI1),and to validate its role in a proliferative vitreoretinopathy(PVR)mouse model.METHODS:Human RPE cell line ARPE-19 cells were treated with TGF-β2 to construct an EMT model.Western blot detected VRK1 level.The effects of VRK1 on SNAI1 expression and biological behavior of ARPE-19 cells were detected by immunofluorescence,ELISA,Transwell,and scratch assay,and the interaction between VRK1 and SNAI1 was confirmed through immunoprecipitation.A PVR mouse model was constructed,and the effects of VRK1 or/and SNAI1 on retinal damage were assessed by pathologic staining.Inflammatory factors and EMT-related proteins were assessed with ELISA and Western blot.RESULTS:VRK1 was upregulated in ARPE-19 cells after TGF-β2 treatment.Overexpression of VRK1 increased cell viability,promoted cell migration and EMT,and the levels of inflammatory factors.Silencing of VRK1 reversed the above indexes.There was a direct interaction between VRK1 and SNAI1,and overexpresssion SNAI1 weakened the impacts of silencing of VRK1.In PVR mice,silencing of VRK1 ameliorated retinal structural damage,decreased proinflammatory factor levels,and suppressed SNAI1 and mesenchymal marker expression.SNAI1 overexpression antagonized the protective effects of silencing VRK1 and exacerbated EMT and inflammatory responses.CONCLUSION:VRK1 plays a key role in retinal structural and inflammatory damage in PVR mice by regulating SNAI1 and mediating TGF-β2-caused EMT and inflammatory responses in RPE cells.
文摘Objectives:The current treatment options and therapeutic targets for triple-negative breast cancer(TNBC),an aggressive subtype of breast cancer(BrCA),are limited.This study aimed to identify novel biomarkers and transcriptional regulatory networks(TRN)inherent in TNBC samples.Methods:We analyzed pan-cancer BrCA datasets from The Cancer Genome Atlas(TCGA)to compare triple-positive breast cancer(TPBC)with TNBC.TRN algorithms and virtual inference of protein-enriched regulon(VIPER)were used to identify master regulators and their target genes.Utilizing TNBC cells(MDA-MB-231 and MDA-MB-468),we validated the relationship of nuclear factor erythroid 2-like 3(NFE2L3)and basic helix-loop-helix family member E 40(BHLHE40)by performing a luciferase assay.The expression levels of these targets were measured after transfections with plasmid and siRNA via qRT-PCR and western blots.The effect of these genes on cell proliferation and migration was studied using phenotypic assays.Results:Using computational approaches,we identified NFE2L3 as a master regulator with BHLHE40 as its target gene.NFE2L3 protein binds to the promoter region of BHLHE40 and regulates its transcriptional activity.Additionally,silencing and overexpressing NFE2L3 and BHLHE40 in TNBC cell lines MDA-MB-231 and MDA-MB-468 showed that NFE2L3 directly regulates BHLHE40 at both transcriptional and translational levels.We found that BHLHE40 requires NFE2L3 for cell proliferation and migration in TNBC.Conclusion:These findings underscore the significance of NFE2L3 and BHLHE40 in TNBC,highlighting NFE2L3’s role in regulating the oncogenic activity of BHLHE40 in TNBC cells.
基金supported by Hebei Natural Science Foundation(H2024206476)Medical Science Research Project of Hebei(20240101).
文摘Background:The regulatory mechanisms governing vasculogenic mimicry(VM)in oral squamous cell carcinoma(OSCC)remain largely undefined.This study aimed to identify critical factors and elucidate the epigenetic mechanisms underlying VM in OSCC.Methods:Bioinformatics analysis was performed utilizing single-cell RNA-seq,bulk RNA-seq,and histone H3 lysine 27 acetylation(H3K27ac)Chromatin Immunoprecipitation(ChIP)-seq data obtained from The Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO)databases.ChIP-qPCR was used to validate the binding of ETS transcription factor ELK4(ELK4)to the dihydrofolate reductase(DHFR)enhancer.In vitro VM formation and invasion of OSCC cells were assessed using Matrigel-based tube formation and Transwell assays,respectively.Results:Elevated expression of VM-related genes predicts unfavorable prognosis in OSCC patients.High-dimensional weighted gene co-expression network analysis(hdWGCNA)identified epithelial subcluster C4 as most strongly associated with VM and metastasis.Three co-expression modules within this subcluster exhibited significant positive correlations with both phenotypic traits.Among the 30 eigengenes from the three modules,DHFR emerged as a key regulator of VM and metastasis.Knockdown or inhibition of DHFR significantly suppressed VM formation and invasion in OSCC cells.Mechanistically,ELK4 activated DHFR transcription through direct binding to its enhancer.DHFR overexpression rescued VM and invasion impairment induced by ELK4 knockdown.Conclusion:DHFR was a pivotal enhancer-regulated gene driving VM and metastasis in OSCC.ELK4 directly binds to DHFR enhancer regions to activate its transcription,thereby promoting these malignant phenotypes.These findings identified the ELK4/DHFR axis as a promising therapeutic target for anti-angiogenic intervention in OSCC.
基金supported by grants from the National Key Research and Development Program of China(Grant Nos.2023YFD2301000,2022YFD2100102)National Natural Science Foundation of China(Grant No.32302616)+1 种基金Shandong Province(Grant No.ZR2023QC032)the Key Research and Development Program of Shandong Province(Grant No.2023CXGC010709).
文摘Chlorogenic acid(CGA),a potent antioxidant with antimicrobial,antiviral,and metabolic regulatory properties,plays multifunctional roles in apple fruit by enhancing postharvest quality,extending shelf life through oxidative stress reduction,and inhibiting enzymatic browning to preserve color,flavor,and nutritional integrity.Despite the established role of hydroxycinnamoyl transferase(HCT)as a rate-limiting enzyme in CGA biosynthesis,the specific HCT gene responsible for this process and its regulatory mechanisms remain elusive.To address this knowledge gap,we systematically investigated CGA accumulation dynamics during apple storage and functionally characterized MdHCT6,a candidate gene within the HCT family.We found that the chlorogenic acid content in apple fruit increased significantly during postharvest storage compared with the initial storage.Transcriptome analysis showed that the expression level of MdHCT6 was significantly higher than that of other HCT homologues,which was consistent with the reverse transcription quantitative PCR(RT-qPCR)results.In vitro enzymatic assays demonstrated that MdHCT6 catalyzes the synthesis of chlorogenic acid using shikimic acid and quinic acid as precursors,while genetic evidence confirmed its role as a key positive regulator of chlorogenic acid accumulation in apples.Furthermore,we identified the transcription factor MdMYB93 as a direct upstream activator of MdHCT6,establishing a regulatory cascade that governs CGA production.This work not only deciphers the molecular hierarchy of CGA biosynthesis in apples but also provides actionable targets for genetic improvement of antioxidant capacity and postharvest resilience in apple germplasm.
基金supported by the National Key Research and Development Program of China(2021YFF1000304)the National Natural Science Foundation of China(32222060)Anhui Agricultural University(RC422404)to J.Y.
文摘Mitochondria are semi-autonomous organelles present in eukaryotic cells,containing their own genome and transcriptional machinery.However,their functions are intricately linked to proteins encoded by the nuclear genome.Mitochondrial transcription termination factors(mTERFs)are nucleic acid-binding proteins involved in RNA splicing and transcription termination within plant mitochondria and chloroplasts.Despite their recognized importance,the specific roles of mTERF proteins in maize remain largely unexplored.Here,we clone and functionally characterize the maize mTERF18 gene.Our findings reveal that mTERF18 mutations lead to severely undifferentiated embryos,resulting in abortive phenotypes.Early kernel exhibits abnormal basal endosperm transfer layer and a significant reduction in both starch and protein accumulation in mterf18.We identify the mTERF18 gene through mapping-based cloning and validate this gene through allelic tests.mTERF18 is widely expressed across various maize tissues and encodes a highly conserved mitochondrial protein.Transcriptome data reveal that mTERF18 mutations disrupt transcriptional termination of the nad6 gene,leading to undetectable levels of Nad6 protein and reduced complex I assembly and activity.Furthermore,transmission electron microscopy observation of mterf18 endosperm uncover severe mitochondrial defects.Collectively,these findings highlight the critical role of mTERF18 in mitochondrial gene transcription termination and its pivotal impact on maize kernel development.
基金supported by grants from the National Natural Science Foundation of China(81871062)Guangdong Basic and Applied Basic Research Foundation(2024A1515012913)+1 种基金the Key Research Foundation of Guangdong Provincial Education Bureau(2023ZDZX2037)the Special Fund of Science and Technology Innovation Cultivation of Guangdong University Students(pdjh2024a238,pdjh2025ak133)。
文摘Dear Editor,Post-traumatic stress disorder(PTSD)is a chronic neuropsychiatric disorder triggered by severe traumatic events,characterized by persistent intrusive memories,emotional dysregulation,hyperarousal,and avoidance behaviors[1,2].PTSD is associated with significant gene expression changes in key brain regions,including the ventral tegmental area(VTA),which may underlie dysregulation of dopaminergic signaling and stress-related behaviors[3].
基金supported by the National Natural Science Foundation of China(Grant No.:62101087)the China Postdoctoral Science Foundation(Grant No.:2021MD703942)+2 种基金the Chongqing Postdoctoral Research Project Special Funding,China(Grant No.:2021XM2016)the Science Foundation of Chongqing Municipal Commission of Education,China(Grant No.:KJQN202100642)the Chongqing Natural Science Foundation,China(Grant No.:cstc2021jcyj-msxmX0834).
文摘Drug repurposing offers a promising alternative to traditional drug development and significantly re-duces costs and timelines by identifying new therapeutic uses for existing drugs.However,the current approaches often rely on limited data sources and simplistic hypotheses,which restrict their ability to capture the multi-faceted nature of biological systems.This study introduces adaptive multi-view learning(AMVL),a novel methodology that integrates chemical-induced transcriptional profiles(CTPs),knowledge graph(KG)embeddings,and large language model(LLM)representations,to enhance drug repurposing predictions.AMVL incorporates an innovative similarity matrix expansion strategy and leverages multi-view learning(MVL),matrix factorization,and ensemble optimization techniques to integrate heterogeneous multi-source data.Comprehensive evaluations on benchmark datasets(Fdata-set,Cdataset,and Ydataset)and the large-scale iDrug dataset demonstrate that AMVL outperforms state-of-the-art(SOTA)methods,achieving superior accuracy in predicting drug-disease associations across multiple metrics.Literature-based validation further confirmed the model's predictive capabilities,with seven out of the top ten predictions corroborated by post-2011 evidence.To promote transparency and reproducibility,all data and codes used in this study were open-sourced,providing resources for pro-cessing CTPs,KG,and LLM-based similarity calculations,along with the complete AMVL algorithm and benchmarking procedures.By unifying diverse data modalities,AMVL offers a robust and scalable so-lution for accelerating drug discovery,fostering advancements in translational medicine and integrating multi-omics data.We aim to inspire further innovations in multi-source data integration and support the development of more precise and efficient strategies for advancing drug discovery and translational medicine.
基金supported by the National Natural Science Foundation of China(U24A20657,82371613 to F.S.82301798)+2 种基金Key Research and Development Program of Zhejiang Province(2023C03035 to F.S.)China Post-doctoral Science Foundation(2022M722767)Fellowship of China National Postdoctoral Program for Innovative Talents(BX20230314)。
文摘Chromatin remodeling and transcriptional reprogramming play critical roles during mammalian meiotic prophase I;however,the precise mechanisms regulating these processes remain poorly understood.Our previous work demonstrated that deletion of heat shock factor 5(HSF5),a member of the heat shock factor family,induces meiotic arrest and male infertility.However,the molecular pathways through which HSF5 governs meiotic progression have not yet been fully elucidated.In this study,a comprehensive multi-omics approach was applied to investigate the role of HSF5 in modulating chromatin dynamics and transcriptional reprogramming during pachynema progression.Analysis of ATAC-seq and single-cell RNA sequencing data revealed significant alterations in chromatin accessibility and disruption of the transcriptional regulatory network(TRN)in Hsf5−/−spermatocytes.Additionally,HSF5 deficiency resulted in defective XY body formation and altered histone modifications.Notably,Hsf5−/−spermatocytes also exhibited abnormal spermatoproteasome activity specifically on sex chromosomes,with evidence indicating that HSF5 may form a complex with USP7 in vivo to suppress H2AK119ub on meiotic sex chromosomes.These findings provide new insights into the complex,multifunctional role of HSF5 in regulating key meiotic events and advancing our understanding of its function during pachynema progression.
基金Supported by the National Key R&D Program of China,No.2022YFC2503700 and No.2022YFC2503703the National Health Commission Key Laboratory of Nuclear Technology Medical Transformation(Mianyang Central Hospital),No.2023HYX005.
文摘BACKGROUND Esophageal cancer(ESCA)poses a significant challenge in oncology because of the limited treatment options and poor prognosis.Therefore,enhancing the therapeutic effects of radiotherapy for ESCA and identifying relevant therapeutic targets are crucial for improving both the survival rate and quality of life of patients.AIM To define the role of the transcription factor Snail family transcriptional repressor 1(SNAI1)in ESCA,particularly its regulation of radiosensitivity.METHODS A comprehensive analysis of TCGA data assessed SNAI1 expression in ESCA.Survival curves correlated SNAI1 levels with radiotherapy outcomes.Colony formation assays,flow cytometry,and a xenograft model were used to evaluate tumor radiosensitivity and apoptosis.Western blot validated protein expression,while Chromatin im-munoprecipitation assays examined SNAI1's role in regulating epithelial-mesenchymal transition(EMT).RESULTS SNAI1 expression in ESCA cell lines and clinical specimens emphasizes its central role in this disease.Elevated SNAI1 expression is correlated with unfavorable outcomes in radiotherapy.Downregulation of SNAI1 enhances the sensitivity of ESCA cells to ionizing radiation(IR),resulting in remarkable tumor regression upon IR treatment in vivo.This study underscores the direct involvement of SNAI1 in the regulation of EMT,particularly under IR-induced conditions.Furthermore,inhibiting deacetylation effectively suppresses EMT,suggesting a potential avenue to enhance the response to radiotherapy in ESCA.CONCLUSION This study highlights SNAI1's role in ESCA radiosensitivity,offering prognostic insights and therapeutic strategies to enhance radiotherapy by targeting SNAI1 and modulating EMT processes.
基金This work was supported by the National High Technology R&D Project of China (No.2002AA207009) and Wuhan Dawn Project for Youth (No. 20035002016-36).
文摘Northern blot analysis was conducted with mitochondrial RNA from seedling leaves, floral buds, and developing seeds of NCa CMS, maintainer line and fertile F1 using ten mitochondrial genes as probes. The results revealed that 9 out of the 10 mitochondrial genes, except for atp6, showed no difference in different tissues of the corresponding materials of NCα CMS system and that they might be constitutively expressed genes. Eight genes, such as orf139, orf222, atpl, cox1, cox2, cob, rm5S, and rm26S, showed no difference among the three tissues of all the materials detected. So the expression of these eight genes was not regulated by nuclear genes and was not tissue-specific. The transcripts of atp9 were identical among different tissues, but diverse among different materials, indicating that transcription of atp9 was neither controlled by nuclear gene nor tissue-specific. Gene atp6 displayed similar transcripts with the same size among different tissues of all the materials but differed in abundance among tissues of corresponding materials and its expression might be tissue-specific under regulation of nuclear gene. Moreover, three transcripts of orf222 were detected in the floral buds of NCa cms and fertile F1, but no transcript was detected in floral buds of the maintainer line.The transcription of orf139 was similar to that of orf222 but only two transcripts of 0.8 kb and 0.6 kb were produced. The atp9 probe detected a single transcript of 0.6 kb in NCa cms and in maintainer line and an additional transcript of 1.2 kb in fertile F1. The relationship of expression of orf222, orf139, and atp9 with NCa sterility was discussed.
基金Supported by the National“863”Program(2006AA10A210)~~
文摘The peaT1 gene fragment was amplified from pGEM-6p-l-peaT1 by PCR, and recovered target gene was cloned into pLexA vector. After digestion and sequencing, the bait vector pLexA-peaT1 was transformed into yeast strain EGY48 [p8op-lacZ] by PEG/LiAC, and the transcriptional activity of bait vector was detected. The results showed that recombinant bait plasmid pLexA-PEMG1 was constructed, for the two bands of recombinant bait plasmid in agarose gel eleetrophoresis were expected after digesting by restriction endonuclease EcoR I and Xho I. Therefore, the recombinant bait plasmid could be used in yeast two-hybrid system to screen a cDNA library.
基金the National Key Research and Development Program of China(2024YFE0102300)National Natural Science Foundation of China(32470578)to Chunli Chen+1 种基金the funding support from the Fundamental Research Funds for the Central Universities(Program No.2662023LXPY003)to Sisi LiuDr.Junli Liu from Durham University for his reviewing on the manuscript.
文摘Auxins were the first of the major plant hormones and played key roles in plant growth and development.Auxin triggered gene expression through several mechanisms.The canonical textbook model is that auxin binds to TIR1/AFB receptors and stabilizes their interaction with Aux/IAA repressors,leading to their ubiquitination and degradation,which results in activation of ARFs transcription factors.The recent study published in Nature by JiíFriml and co-authors updated the view on gene expression regulated by auxin.The role of TIR-produced cAMP was confirmed to be the second messenger in transcriptional auxin signaling.The conclusions raised in this Nature article shift the paradigm about the regulation of plant growth and development by auxin to the modulation of cAMP production and its interaction with candidate targets.
基金supported by grants from the National Natural Science Foundation of China(Grant Nos.32025032 and 32202415)the Agricultural Breeding Project of Ningxia Hui Autonomous Region(Grant No.NXNYYZ20210104)the National Key Research and Development Program of China(Grant No.2022YFE0116400).
文摘In climacteric fruits,the role of ethylene in promoting ripening process and its molecular regulatory mechanisms have been well elucidated.However,research into ethylene's roles in non-climacteric fruits has only advanced in recent years,largely because these fruits produce much less ethylene than climacteric fruits.Consequently,reports on its molecular regulatory involvement are still limited.Grape(Vitis vinifera L.),one of the most economically valuable fruits,is regarded as a classical non-climacteric fruit.In this study,an enzyme participating in the last step of ethylene biosynthesis,VvACO1,has been identified as a key enzyme controlling ethylene release in grape fruits(Vitis vinifera‘Jingyan’and‘Red Balado’)using correlation analysis and enzymatic experiments.The transcriptional regulation of VvACO1 was investigated by integrating multiple methods such as DNA pull-down assays,co-expression analysis,dual luciferase reporting system,yeast one-hybrid assays,and transgenic experiments.Our findings revealed that the upregulation of VvACO1 in grape fruits was primarily caused by the removal of transcriptional inhibition.Remarkably,seven transcription factors(TFs)were identified as inhibitors of VvACO1,including VvHY5 from bZIP family,VvWIP2 from C2H2 family,VvBLH1 from Homeobox family,VvAG1 and VvCMB1 from MADS-box family,VvASIL1 and VvASIL2 from Trihelix family.These seven TFs were located in nuclei and exhibited transcriptional inhibition activity.Notably,VvAG1 and VvASIL2 could inhibit VvACO1 expression when overexpressed in grape leaves.Our findings provided theoretical clues for differences of ethylene release regulation between climacteric and non-climacteric fruits,also the identified seven TFs could be potential targets for grape molecular breeding.
基金supported by the National Key R&D Program of China(Grant no.2022YFC2807502)Qingdao Marine Science and Technology Center(Grant no.2022QNLM030003-1)Taishan Scholar Distinguished Expert Program in Shandong Province(Grant no.tstp20240504).
文摘A polyketide synthase-nonribosomal peptide synthetase gene cluster twn in Talaromyces sp.HDN1820200 was activated by overexpression of the pathway-specific transcriptional factor TwnD.Large-scale fermentation and chemical investigation of the mutant strain HDN1820200/TwnD led to the discovery of one new polyketide-amino acid conjugate,bipolamide C and one new polyketide compound,variotin A.The structures of the new compounds were determined by nuclear magnetic resonance(NMR)analysis,high-resolution electrospray ionization mass spectrometry,feeding experiments,NMR calculation and DP4^(+)analysis.This study revealed that the overexpression of the pathway-specific transcriptional factor represents a promising approach for the discovery of new natural products in fungi within specialized habitat.
基金supported by the National Natural Science Foundation of China[grant numbers 32271914 and 32301660]the Quality Engineering Project of Anhui Provincial Department of Education[grant number 2023zygzts007].
文摘Acer paxii belongs to the evergreen species of Acer,but it exhibits a unique feature of reddish leaves in fall in subtropical regions.Although the association of AP2/ERF transcription factors with color change has been well-documented in prior research,molecular investigations focusing on AP2/ERF remain notably lacking in Acer paxii.This research focuses on performing an extensive genome-wide investigation to identify and characterize the AP2/ERF gene family in Acer paxii.As a result,123 ApAP2/ERFs were obtained.Phylogenetic analyses categorized the ApAP2/ERF family members into 15 subfamilies.The evolutionary traits of the ApAP2/ERFs were investigated by analyzing their chromosomal locations,conserved proteinmotifs,and gene duplication events.Moreover,investigating gene promoters revealed their potential involvement in developmental regulation,physiological processes,and stress adaptationmechanisms.Measurements of anthocyanin content revealed a notable increase in red leaves during autumn.Utilizing transcriptome data,transcriptomic profiling revealed that the majority of AP2/ERF genes in Acer paxii displayed significant differential expression between red and green leaves during the color-changing period.Furthermore,through qRT-PCR analysis,it was found that the gene expression levels of ApERF006,ApERF014,ApERF048,ApERF097,and ApERF107 were significantly elevated in red leaves.This indicates their potential participation in leaf pigmentation processes.These findings offer significant insights into the biological significance of ApAP2/ERF transcription factors and lay the groundwork for subsequent investigations into their regulatorymechanisms underlying leaf pigmentation in Acer paxii.
基金funded by the National Key R&D Program of China(2023YFD1401401)the China Agriculture Research System(CARS27)。
文摘Defensin,an essential component of plant development,is indispensable in pathogen resistance.However,the molecular function of defensins under pathological conditions of Cytospora canker has not been characterized in apple plants.The present study exhibits a detailed overview of the phylogeny and structure of 29 defensins(MdDEF)in apple.Expression analysis revealed that MdDEF genes were spatiotemporally diverse across apple tissues.Five MdDEF genes were found to be significantly up-regulated following a challenge with Cytospora mali.The transgenic overexpression of five defensin genes in apple calli enhanced resistance to C.mali.Among them,MdDEF30 was strongly induced and conferred the highest resistance level in vivo.Meanwhile,antifungal activity assays in vitro demonstrated that a recombinant protein produced from MdDEF30could inhibit the growth of C.mali.Notably,MdDEF30 promoted the accumulation of reactive oxygen species(ROS)and activated defense-related genes such as PR4,PR10,CML13,and MPK3.Co-expression regulatory network analysis showed that MdWRKY75 may regulate the expression of MdDEF30.Further yeast onehybrid(Y1H),luciferase,and chromatin Immunoprecipitation quantitative polymerase chain reaction(ChIPqPCR)assays verified that MdWRKY75 could directly bind to the promoter of MdDEF30.Importantly,pathogen inoculation assays confirmed that MdWRKY75 positively regulates resistance by transcriptionally activating MdDEF30.Overall,these results demonstrated that MdDEF30 promotes resistance to C.mali in apple plants and that MdWRKY75 regulates MdDEF30 expression during the induction of resistance,thereby clarifying biochemical mechanisms of resistance to C.mali in apple trees.
文摘Since transgene silencing was found in transgenic plants,many scholars have studied it extensively and considered that it has three functional mechanisms:post dependent gene silencing,transcriptional gene silencing,post transcriptional gene silencing.At the moment,people have mainly focused on the study of post transcriptional gene silencing and found its features:extensivity,conduction and peculiarity,also put forward some hypothesis for its mechanisms,for example,RNA threshold model,aberrant RNA model,inter or intra molecular base pairing model and so on.Furthermore,post transcriptional gene silencing is being applied in gene engineering of plants.Recently the people have found that post transcriptional gene silencing has bearing on capacity plants resisting virus.Many researchers have studied post transcriptional gene silencing,but there are some questions which need be solved in the future.This article summarizes progresses in features,mechanisms,applies of post transcriptional gene silencing about transgenic plants.
文摘While human immunodeficiency virus 1(HIV-1) infectionis controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from the body. Despite decades of research there is still no effective vaccine to prevent HIV-1 infection. Therefore, the possibility of an RNA interference(RNAi)-based cure has become an increasingly explored approach. Endogenous gene expression is controlled at both, transcriptional and post-transcriptional levels by noncoding RNAs, which act through diverse molecular mechanisms including RNAi. RNAi has the potential to control the turning on/off of specific genes through transcriptional gene silencing(TGS), as well as finetuning their expression through post-transcriptional gene silencing(PTGS). In this review we will describe in detail the canonical RNAi pathways for PTGS and TGS, the relationship of TGS with other silencing mechanisms and will discuss a variety of approaches developed to suppress HIV-1 via manipulation of RNAi. We will briefly compare RNAi strategies against other approaches developed to target the virus, highlighting their potential to overcome the major obstacle to finding a cure, which is the specific targeting of the HIV-1 reservoir within latently infected cells.
文摘As part of our efforts to identify novel contraceptive targets in the epididymis we performed transcriptional profiling on each of the 10 and 19 segments of the mouse and rat epididymidis, respectively, using Affymetrix whole genome microarrays. A total of 17 096 and 16 360 probe sets representing transcripts were identified as being expressed in the segmented mouse and rat epididymal transcriptomes, respectively. Comparison of the expressed murine transcripts against a mouse transcriptional profiling database derived from 22 other mouse tissues identified 77 transcripts that were expressed uniquely in the epididymis. The expression of these genes was further evaluated by reverse transcription polymerase chain reaction （RT-PCR） analysis of RNA from 21 mouse tissues. RT-PCR analysis confirmed epididymis-specific expression of Defensin Beta 13 and identified two additional genes with expression restricted only to the epididymis and testis. Comparison of the 16 360 expressed transcripts in the rat epididymis with data of 21 other tissues from a rat transcriptional profiling database identified 110 transcripts specific for the epididymis. Sixty-two of these transcripts were further investigated by qPCR analysis. Only Defensin 22 （E3 epididymal protein） was shown to be completely specific for the epididymis. In addition, 14 transcripts showed more than 100-fold selective expression in the epididymis. The products of these genes might play important roles in epididymal and/or sperm function and further investigation and validation as contraceptive targets are warranted. The results of the studies described in this report are available at the Mammalian Reproductive Genetics （MRG） Database （http：//mrg. genetics.washington.edu/）. （Asian J Androl 2007July; 9： 522-527）
基金supported by the National Natural Science Foundation of China (31871634, 31500985)
文摘Retrotransposons account for a large proportion of the genome and genomic variation, and play key roles in creating novel genes and diversifying the genome in many eukaryotic species. Although retrotransposons are abundant in plants, their roles had been underestimated because of a lack of research. Here, we characterized a gibberellin Acid (GA)-insensitive dwarf mutant, 84133, in foxtail millet. Map-based cloning revealed a 5.5-kb Copia-like retrotransposon insertion in DWARF1 (D1), which encodes a DELLA protein. Transcriptional analysis showed that the Copia retrotransposon mediated the transcriptional reprogramming of D1 leading to a novel N-terminal-deleted truncated DELLA transcript that was putatively driven by Copia's LTR, namely D1-TT, and another chimeric transcript. The presence of D1-TT was confirmed by protein immunodetection analysis. Furthermore, D1-TT protein was resistant to GA3 treatment compared with the intact DELLA protein due to its inability to interact with the GA receptor, SiGID1. Overexpression of D1-TT in foxtail millet resulted in dwarf plants, confirming that it determines the dwarfism of 84133. Thus, our study documents a rare instance of long terminal repeat (LTR) retrotransposon-mediated transcriptional reprograming in the plant kingdom. These results shed light on the function of LTR retrotransposons in generating new gene functions and genetic diversity.
