One of the main diseases that adversely impacts the global citrus industry is citrus bacterial canker(CBC),caused by the bacteria Xanthomonas citri subsp.citri(Xcc).Response to CBC is a complex process,with both prote...One of the main diseases that adversely impacts the global citrus industry is citrus bacterial canker(CBC),caused by the bacteria Xanthomonas citri subsp.citri(Xcc).Response to CBC is a complex process,with both proteinDNA as well as protein–protein interactions for the regulatory network.To detect such interactions in CBC resistant regulation,a citrus high-throughput screening system with 203 CBC-inducible transcription factors(TFs),were developed.Screening the upstream regulators of target by yeast-one hybrid(Y1H)methods was also performed.A regulatory module of CBC resistance was identified based on this system.One TF(CsDOF5.8)was explored due to its interactions with the 1-kb promoter fragment of CsPrx25,a resistant gene of CBC involved in reactive oxygen species(ROS)homeostasis regulation.Electrophoretic mobility shift assay(EMSA),dual-LUC assays,as well as transient overexpression of CsDOF5.8,further validated the interactions and transcriptional regulation.The CsDOF5.8–CsPrx25 promoter interaction revealed a complex pathway that governs the regulation of CBC resistance via H2O2homeostasis.The high-throughput Y1H/Y2H screening system could be an efficient tool for studying regulatory pathways or network of CBC resistance regulation.In addition,it could highlight the potential of these candidate genes as targets for efforts to breed CBC-resistant citrus varieties.展开更多
Allium senescens,is an important economic and ecological grassland plant with drought-resistant characteristics.A TCP protein transcription factor is important in the regulation of plant development and adverse respon...Allium senescens,is an important economic and ecological grassland plant with drought-resistant characteristics.A TCP protein transcription factor is important in the regulation of plant development and adverse responses.However,the mechanism by which TCP transcription functions in drought resistance in Allium senescens is still not clear.Here,we obtained a total of 190,305 transcripts with 115,562 single gene clusters based on RNA-Seq sequencing of Allium senescens under drought stress.The total number of bases was 97,195,096 bp,and the average length was 841.06 bp.Furthermore,we found that there were eight genes of the TCP family that showed an upregulated expression trend under drought stress in Allium senescens.We carried out an investigation to determine the evolution and function of the AsTCP family and how they produce an effect in drought resistance.The 14 AsTCP genes were confirmed and divided into class I and class II containing CIN and CYC/TBI subfamilies,respectively.We also found that the expression of AsTCP17 was remarkably upregulated with drought treatment.Besides,the transformation of AsTCP17 in Arabidopsis revealed that the protective enzymes,namely polyphenol oxidase(POD)and superoxide dismutase(SOD),were increased by 0.4 and 0.8 times,respectively.Chlorophyll content was also increased,while the H2O2 and malondialdehyde(MDA)contents were decreased.Staining assays with 3,3′-diaminobenzidine(DAB)also suggested that the AsTCP17 downregulates reactive oxygen species(ROS)accumulation.In addition,overexpression of the AsTCP17 affected the accumulation of drought-related hormones in plants,and the synthesis of ABA.The expression of AtSVP and AtNCED3,related ABA synthesis pathway genes,indicated that the level of expression of AtSVP and AtNCED3 was obviously enhanced,with the overexpression of line 6 showing a 20.6-fold and 7.0-fold increase,respectively.Taken together,our findings systematically analyze the AsTCPs family at the transcriptome expression level in Allium senescens,and we also demonstrated that AsTCP17 protein,as a positive regulator,was involved in drought resistance of Allium senescens.In addition,our research contributes to the comprehensive understanding of the drought stress defense mechanism in herbaceous plants.展开更多
Apple(Malus domestica)fruit generally undergoes a climacteric.During its ripening process,there is a peak in ethylene release and its firmness simultaneously decreases.Although more in-depth research into the mechanis...Apple(Malus domestica)fruit generally undergoes a climacteric.During its ripening process,there is a peak in ethylene release and its firmness simultaneously decreases.Although more in-depth research into the mechanism of climacteric-type fruit ripening is being carried out,some aspects remain unclear.In this study,we compared the transcriptomes of 0-Pre and 15-Post(pre-and post-climacteric fruit),and 15-Post and 15-MCP[fruit treated with 1-MCP(1-methylcyclopropene)].Various transcription factors,such as MADS-box,ERF,NAC,Dof and SHF were identified among the DEGs(differential gene expressions).Furthermore,these transcription factors were selected for further validation analysis by qRT-PCR.Moreover,yeast one hybrid(Y1H),β-glucuronidase(GUS)transactivation assay and dual-luciferase reporter assay showed that MdAGL30,MdAGL104,MdERF008,MdNAC71,MdDof1.2,MdHSFB2a and MdHSFB3 bound to MdACS1 promoter and directly regulated its transcription,thereby regulating ethylene biosynthesis in apple fruit.Our results provide useful information and new insights for research on apple fruit ripening.展开更多
WRKY transcription factors(TFs)have been identified as important core regulators in the responses of plants to biotic and abiotic stresses.Cultivated peanut(Arachis hypogaea)is an important oil and protein crop.Previo...WRKY transcription factors(TFs)have been identified as important core regulators in the responses of plants to biotic and abiotic stresses.Cultivated peanut(Arachis hypogaea)is an important oil and protein crop.Previous studies have identified hundreds of WRKY TFs in peanut.However,their functions and regulatory networks remain unclear.Simultaneously,the AdWRKY40 TF is involved in drought tolerance in Arachis duranensis and has an orthologous relationship with the AhTWRKY24 TF,which has a homoeologous relationship with AhTWRKY106 TF in A.hypogaea cv.Tifrunner.To reveal how the homoeologous AhTWRKY24 and AhTWRKY106 TFs regulate the downstream genes,DNA affinity purification sequencing(DAP-seq)was performed to detect the binding sites of TFs at the genome-wide level.A total of 3486 downstream genes were identified that were collectively regulated by the AhTWRKY24 and AhTWRKY106 TFs.The results revealed that W-box elements were the binding sites for regulation of the downstream genes by AhTWRKY24 and AhTWRKY106 TFs.A gene ontology enrichment analysis indicated that these downstream genes were enriched in protein modification and reproduction in the biological process.In addition,RNA-seq data showed that the AhTWRKY24 and AhTWRKY106 TFs regulate differentially expressed genes involved in the response to drought stress.The AhTWRKY24 and AhTWRKY106 TFs can specifically regulate downstream genes,and they nearly equal the numbers of downstream genes from the two A.hypogaea cv.Tifrunner subgenomes.These results provide a theoretical basis to study the functions and regulatory networks of AhTWRKY24 and AhTWRKY106 TFs.展开更多
Molecular mechanisms of the Kruppel-like family of transcription factors (KLFs) have been studied more in proliferating cells than in post-mitotic cells such as neurons. We recently found that KLFs regulate intrinsi...Molecular mechanisms of the Kruppel-like family of transcription factors (KLFs) have been studied more in proliferating cells than in post-mitotic cells such as neurons. We recently found that KLFs regulate intrinsic axon growth ability in central nervous system (CNS) neurons in- cluding retinal ganglion cells, and hippocampal and cortical neurons. With at least 15 of 17 KLF family members expressed in neurons and at least 5 structurally unique subfamilies, it is import- ant to determine how this complex family functions in neurons to regulate the intricate genetic programs of axon growth and regeneration. By characterizing the molecular mechanisms of the KLF family in the nervous system, including binding partners and gene targets, and comparing them to defined mechanisms defined outside the nervous system, we may better understand how KLFs regulate neurite growth and axon regeneration.展开更多
Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 f...Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species.Whole-genome duplication(WGD)was the dominant event type in almost all Cucurbitaceae plants.The TF families were divided into 1210 orthogroups(OGs),of which,112 were unique to Cucurbitaceae.Although the loss of several gene families was detected in Cucurbitaceae,the gene families expanded in five species that experienced a WGD event comparing with grape.Our findings revealed that the recent WGD events that had occurred in Cucurbitaceae played important roles in the expansion of most TF families.The functional enrichment analysis of the genes that significantly expanded or contracted uncovered five gene families,AUX/IAA,NAC,NBS,HB,and NF-YB.Finally,we conducted a comprehensive analysis of the TCP gene family and identified 16 tendril-related(TEN)genes in 11 Cucurbitaceae species.Interestingly,the characteristic sequence changed from CNNFYFP to CNNFYLP in the TEN gene(Bhi06M000087)of Benincasa hispida.Furthermore,we identified a new characteristic sequence,YNN,which could be used for TEN gene exploitation in Cucurbitaceae.In conclusion,this study will serve as a reference for studying the relationship between gene family evolution and genome duplication.Moreover,it will provide rich genetic resources for functional Cucurbitaceae studies in the future.展开更多
AIM: To investigate the gene expression pattern of hepatocyte nuclear factor 6 (HNF6) and other liverenriched transcription factors in various segments of the human intestine to better understand the differentiation o...AIM: To investigate the gene expression pattern of hepatocyte nuclear factor 6 (HNF6) and other liverenriched transcription factors in various segments of the human intestine to better understand the differentiation of the gut epithelium. METHODS: Samples of healthy duodenum and jejunum were obtained from patients with pancreatic cancer whereas ileum and colon was obtained from patients undergoing right or left hemicolectomy or (recto)sigmoid or rectal resection. All surgical specimens were subjected to histopathology. Excised tissue was shock-frozen and analyzed for gene expression of liver-enriched transcription factors by semiquantitative reverse transcription polymerase chain and compared to the human colon carcinoma cell line Caco-2. Protein expression of major liver-enriched transcription factors was determined by Western blotting while the DNA binding of HNF6 was investigated by electromobility shift assays. RESULTS: The gene expression patterning of liverenriched transcription factors differed in the various segments of the human intestine with HNF6 gene expression being most abundant in the duodenum (P < 0.05) whereas expression of the zinc finger protein GATA4 and of the HNF6 target gene ALDH3A1 was most abundant in the jejunum (P < 0.05). Likewise, expression of FOXA2 and the splice variants 2 and 4 of HNF4α were most abundantly expressed in the jejunum (P < 0.05). Essentially, expression of transcription factors declined from the duodenum towards the colon with the most abundant expression in the jejunum and less in the ileum. The expression of HNF6 and of genes targeted by this factor, i.e. neurogenin 3 (NGN3) was most abundant in the jejunum followed by the ileum and the colon while DNA binding activity of HNF4α and of NGN3 was conf irmed by electromobility shift assays to an optimized probe. Furthermore, Western blotting provided evidence of the expression of several liver-enriched transcription factors in cultures of colon epithelial cells, albeit at different levels. CONCLUSION: We describe significant local and segmental differences in the expression of liver-enriched transcription factors in the human intestine which impact epithelial cell biology of the gut.展开更多
Glioblastoma(GBM)is the most common,most aggressive and deadliest brain tumor.Recently,remarkable progress has been made towards understanding the cellular and molecular biology of gliomas.GBM tumor initiation,progres...Glioblastoma(GBM)is the most common,most aggressive and deadliest brain tumor.Recently,remarkable progress has been made towards understanding the cellular and molecular biology of gliomas.GBM tumor initiation,progression and relapse as well as resistance to treatments are associated with glioma stem cells(GSCs).GSCs exhibit a high proliferation rate and self-renewal capacity and the ability to differentiate into diverse cell types,generating a range of distinct cell types within the tumor,leading to cellular heterogeneity.GBM tumors may contain different subsets of GSCs,and some of them may adopt a quiescent state that protects them against chemotherapy and radiotherapy.GSCs enriched in recurrent gliomas acquire more aggressive and therapy-resistant properties,making them more malignant,able to rapidly spread.The impact of SOX transcription factors(TFs)on brain tumors has been extensively studied in the last decade.Almost all SOX genes are expressed in GBM,and their expression levels are associated with patient prognosis and survival.Numerous SOX TFs are involved in the maintenance of the stemness of GSCs or play a role in the initiation of GSC differentiation.The fine-tuning of SOX gene expression levels controls the balance between cell stemness and differentiation.Therefore,innovative therapies targeting SOX TFs are emerging as promising tools for combatting GBM.Combatting GBM has been a demanding and challenging goal for decades.The current therapeutic strategies have not yet provided a cure for GBM and have only resulted in a slight improvement in patient survival.Novel approaches will require the fine adjustment of multimodal therapeutic strategies that simultaneously target numerous hallmarks of cancer cells to win the battle against GBM.展开更多
This study was conducted to determine the effects of varying the ratio of lysine to digestible energy level On the activity and gene expression of the transcription factors peroxisome proliferator-activated receptor-...This study was conducted to determine the effects of varying the ratio of lysine to digestible energy level On the activity and gene expression of the transcription factors peroxisome proliferator-activated receptor-γ (PPAR-γ) and CCAAT/enhancer-binding protein-or and -β (C/EBP-α and C/EBP-β) to better understand the regulatory mechanisms controlling adipogenesis in fat and muscle tissue of the Rongchang pig. A total of 144 castrated Rongchang pigs weighing approximately 20 kg were used in a 2 ×2 factorial design experiment. Diets were formulated to contain a high (14.22 MJ/kg) or low (13.11 MJ/kg) digesti- ble energy (DE) level. Within each energy level, pigs were fed diets containing a high lysine: DE ratio (0.67,0. 53, or 0. 42) or a low lysine : DE ratio (0.49,0.38 ,or 0.30) during the periods from 20 to 50 kg, 50 to 80 kg, and 80 kg to slaughter, respectively. Each diet was fed to six replicate pens, each containing nine pigs. When the pigs reached average live weights of 20,35,60, and 90 kg ,one pig from each of the replicates was chosen at random and slaughtered.Samples of back fat and longissimus dorsi muscle were collected for the assessment of transcriptional factor. The results showed that feeding a high DE level significantly increased ( P 〈 0.05 ) the expression of PPAR-T at 60 and 90 kg in muscle and at 35,60, and 90 kg in back fat. Energy level also significantly increased the expression of C/EBP-fl at 35 and 60 kg in both muscle and back fat ( P 〈 0.05 ). Higher dieta- ry lysine increased the expression of C/EBP-fl in muscle at 35 and 90 kg ( P 〈 0.05), but decreased the expression in back fat at 35 (P = 0.03 ) and 90 kg (P = 0.09). The lysine level increased the expression of PPAR-3~ in muscle at 60 kg only. Energy level and lysine content had no significant effects on promote the activity of PPAR-γ, C/EBP-α, or C/EBP-β either in muscle or in back fat at any level of the body weights tested. Collectively, these data indicated that dietary energy density and lysine level were equally important for lipid deposition in muscle tissue, whereas dietary energy density was more important than lysine level for fat deposition in fat tissue.展开更多
Background: The use of equine bone marrow mesenchymal stem cells (BMSC) is a novel method to improve fracture healing in horses. However, additional research is needed to identify optimal culture conditions and to ...Background: The use of equine bone marrow mesenchymal stem cells (BMSC) is a novel method to improve fracture healing in horses. However, additional research is needed to identify optimal culture conditions and to determine the mechanisms involved in regulating BMSC differentiation into osteoblasts. The objectives of the experiments were to determine: 1) if autologous or commercial serum is better for proliferation and differentiation of equine BMSC into osteoblasts, and 2) the expression of key transcription factors during the differentiation of equine BMSC into osteoblasts. Equine BMSC were isolated from the sterna of 3 horses, treated with purchased fetal bovine serum (FBS) or autologous horse serum (HS), and cell proliferation determined. To induce osteoblast differentiation, cells were incubated with L-ascorbic acid-2-phosphate and glycerol-2-phosphate in the presence or absence of human bone morphogenetic protein2 (BMP2), dexamethasone (DEX), or combination of the two. Alkaline phosphatase (ALP) activity, a marker of osteoblast differentiation, was determined by ELISA. Total RNA was isolated from differentiating BMSC between d 0 to 18 to determine expression of runt-reloted tronscrJption foctor2 (Runx2), osterix (Osx), and T-box3 (Tbx3). Data were analyzed by ANOVA. Results: Relative to control, FBS and HS increased cell number (133 ± 5 and 116 ± 5%, respectively; P 〈 0.001) and 5-bromo- 2'-deoxyuridine (BrdU) incorporation (167 ± 6 and 120 ± 6%, respectively; P 〈 0.001). Treatment with DEX increased ALP activity compared with control (1,638 ± 38%; P 〈 0.001). In the absence and presence of Dex, BMP-2 did not alter ALP activity (P 〉 0.8). Runt-reloted transcription foctor2 expression increased 3-fold (P 〈 0.001) by d 6 of culture. Osterix expression increased 94old (P 〈 0.05) by d 18 of culture. Expression of Tbx3 increased 1.8-fold at d 3 (P 〈 0.01); however expression was reduced 4-fold at d 18 (P 〈 0.01). Conclusions: Dexamethasone, but not BMP-2, is required for differentiation of equine BMSC into osteoblasts. In addition, expression of Runx2 and osterix increased and expression of Tbx3 is reduced during differentiation.展开更多
AIMTo investigate the expression of transcription factors Slug in human lens epithelial cells (HLECs) undergoing epithelial-mesenchymal transition (EMT) induced by connective tissue growth factor (CTGF).METHODSHLECs w...AIMTo investigate the expression of transcription factors Slug in human lens epithelial cells (HLECs) undergoing epithelial-mesenchymal transition (EMT) induced by connective tissue growth factor (CTGF).METHODSHLECs were treated with CTGF of different concentrations (20, 50 and 100 ng/mL) or without CTGF (control) for 24h. The morphological changes of HLECs were analysed by microscopy. The expression and cellular localization of Slug was evaluated by immumo-fluorescence. Expressions of Slug, E-cadherin and alpha smooth muscle actin (α-SMA) were further determined by Western blot analysis.RESULTSHLECs showed spidle fibrolasts-like characteristics and loosely connected each other after CTGF treatment. The immuno-fluorescence staining indicated that Slug was localized in the nuclei and its expression was induced by CTGF. The relative expressions of Slug protein were 1.64±0.11, 1.96 ±0.03, 3.12 ±0.10, and 4.08±0.14, respectively, in response to control group and treatment with CTGF of 20, 50 and 100 ng/mL (F=443.86, P<0.01). The increased Slug protein levels were correlated well with up-expression of α-SMA (0.78±0.05, 0.85±0.06, 2.17±0.15, 2.86±0.10; F=449.85, P<0.01) and down-expression of E-cadherin (2.50±0.11, 1.79±0.26, 1.05±0.14, 0.63±0.08; F=101.55, P<0.01).CONCLUSIONTranscription factor Slug may be involved in EMT of HLECs induced by CTGF in vitro.展开更多
Specificity protein(Sp)transcription factors(TFs)Sp1,Sp3 and Sp4,and the orphan nuclear receptor 4A1(NR4A1)are highly expressed in pancreatic tumors and Sp1 is a negative prognostic factor for pancreatic cancer patien...Specificity protein(Sp)transcription factors(TFs)Sp1,Sp3 and Sp4,and the orphan nuclear receptor 4A1(NR4A1)are highly expressed in pancreatic tumors and Sp1 is a negative prognostic factor for pancreatic cancer patient survival.Results of knockdown and overexpression of Sp1,Sp3 and Sp4 in pancreatic and other cancer lines show that these TFs are individually pro-oncogenic factors and loss of one Sp TF is not compensated by other members.NR4A1 is also a prooncogenic factor and both NR4A1 and Sp TFs exhibit similar functions in pancreatic cancer cells and regulate cell growth,survival,migration and invasion.There is also evidence that Sp TFs and NR4A1 regulate some of the same genes including survivin,epidermal growth factor receptor,PAX3-FOXO1,α5-andα6-integrins,β1-,β3-andβ4-integrins;this is due to NR4A1 acting as a cofactor and mediating NR4A1/Sp1/4-regulated gene expression through GC-rich gene promoter sites.Several studies show that drugs targeting Sp downregulation or NR4A1 antagonists are highly effective inhibitors of Sp/NR4A1-regulated pathways and genes in pancreatic and other cancer cells,and the triterpenoid celastrol is a novel dual-acting agent that targets both Sp TFs and NR4A1.展开更多
Larix olgensis A.Henry is a fast-growing tree used for aff orestation in northeastern China and has great ecological and economic value.For studying developmental genes in the xylem of this species,we investigated the...Larix olgensis A.Henry is a fast-growing tree used for aff orestation in northeastern China and has great ecological and economic value.For studying developmental genes in the xylem of this species,we investigated the Myb transcription factor family,one of the largest families of transcription factors in plants,which plays an important role in the regulation of lignifi cation in plant secondary walls.By sequencing a L.olgensis cDNA library using the Illumina HiSeq2500 high-throughput sequencing platform,we obtained 58,683 unigene sequences,of which 16,554 unigenes were longer than 1000 bp,accounting for 28.2%of the total database.The alignment of these genes with the GO,COG,KEGG,Swiss-Prot and NR databases resulted in annotated 29,350 unigenes.We obtained a total of 1460 differentially expressed genes,of which 453 were upregulated and 1007 were downregulated at the two developmental stages analyzed.The gene annotations showed a wide range of biological functions and metabolic pathways.The 10 Myb transcription factors that were obtained from the diff erentially expressed genes were analyzed by real-time quantitative PCR(qRT-PCR).The results showed that four Myb transcription factors may be associated with xylem development in L.olgensis.Due to the large genome size of conifers,genomics research on these species has lagged behind that for other plant groups.Our data provide the basis for further studies on xylem development in L.olgensis.展开更多
The retina and its development: The retina is an essential part of the visual system. A myriad of eye diseases are characterized by retinal degeneration, caused by either genetic or environmental factors. This unders...The retina and its development: The retina is an essential part of the visual system. A myriad of eye diseases are characterized by retinal degeneration, caused by either genetic or environmental factors. This underscores the importance of studying the genetic and molecular mechanisms that regulate the generation and maintenance of neurons in the mammalian retina. Our recent studies demonstrate that two related transcription factors Onecutl (Ocl) and Onecut2 (0c2) regulate multiple cell fates in the mouse retina, and their absence results in progressive retinal neurodegeneration (Wu et al., 2012, 2013; Sapkota et al., 2014).展开更多
Diseases and disorders of the central nervous system often require significant interventions to restore lost function due to their com- plexity. Examples of such disorders include Parkinson's disease, Alzheimer's di...Diseases and disorders of the central nervous system often require significant interventions to restore lost function due to their com- plexity. Examples of such disorders include Parkinson's disease, Alzheimer's disease, multiple sclerosis, traumatic brain injury, and spinal cord in)ury. These diseases and disorders result trom healthy cells being destroyed, which in turn causes dysfunction in the cen- tral nervous system, The death of these cells can trigger a cascade of events that affect the rest of the body, causing symptoms that become progressively worse over time. Developing strategies for repairing the damage to the central nervous system remains chal- lenging, in part due to its inability to regenerate.展开更多
Background/Aim: MicroRNAs with regulatory functions in gene expression are implicated in different diseases. The present study investigated differentially expressed miRNAs that possibly influence transcription factors...Background/Aim: MicroRNAs with regulatory functions in gene expression are implicated in different diseases. The present study investigated differentially expressed miRNAs that possibly influence transcription factors involved in insulin gene expression in Chronic Pancreatitis (CP) employing bioinformatics approaches. Methods: Pancreatic tissues were collected from CP patients undergoing partial pancreatectomy (n = 16) and controls (n = 15) undergoing resections for non-pancreatic malignancies. MiRNA profiles obtained using microarrays were validated by qRT-PCR. Target search involving miRWalk and TarBase as well as functional annotation employing KEGG (Kyoto encyclopedia of genes and genomes) and DAVID (Database for Annotation) databases were performed. Ingenuity pathway analysis (IPA) was used to construct networks relating miRNAs to their target genes. mRNA and proteins related to insulin gene transcription factors and hormones were evaluated by qRT-PCR and western blotting followed by confirmation upon immunofluorescent staining. Results: Microarray data revealed 10 up-regulated and 15 down-regulated miRNAs in CP as compared to controls (Log2 FC > 2). Bioinformatic analysis showed 8399 target genes and KEGG pathway analysis suggested a role for the dysregulated miRNAs in modulating cytokine signaling, fibrosis, JAK-STAT signaling and insulin synthesis. IPA analysis suggested a simplified network attributing dysregulated miRNAs to NFκB-dependent cytokine signaling. Further, associations could be noted between miRNA 200b with Maf A, 138-1 with Neuro D and 27b with FoxO1. Decreases in mRNA levels of Pdx1, Neuro D and increases of Maf A and FoxO1 transcription factors could be noted (P Conclusion: Our results identified dysregulation of miRNAs 138-1, 27b and 200b which were found to be associated with insulin gene transcription factors Neuro D, FoxO1 and Maf A respectively.展开更多
The highbush blueberry(Vaccinium corymbosum),Duke,was used to construct a de novo transcriptome sequence library and to perform data statistical analysis.Mega 4,CLC Sequence Viewer 6 software,and quantitative PCR we...The highbush blueberry(Vaccinium corymbosum),Duke,was used to construct a de novo transcriptome sequence library and to perform data statistical analysis.Mega 4,CLC Sequence Viewer 6 software,and quantitative PCR were employed for bioinformatics and expression analyses of the basic helix-loop-helix(BHLH)transcription factors of the sequencing library.The results showed that 28.38 gigabytes of valid data were obtained from transcriptome sequencing and were assembled into 108 033 unigenes.Functional annotation showed that 32 244 unigenes were annotated into Clusters of Orthologous Groups(COG)and Gene Ontology(GO)databases,whereas the rest of the 75 789 unigenes had no matching information.By using COG and GO classification tools,sequences with annotation information were divided into 25 and 52 categories,respectively,which involved transport and metabolism,transcriptional regulation,and signal transduction.Analysis of the transcriptome library identified a total of 59 BHLH genes.Sequence analysis revealed that 55 genes of that contained a complete BHLH domain.Furthermore,phylogenetic analysis showed that BHLH genes of blueberry(Duke)could be divided into 13 sub-groups.PCR results showed that 45 genes were expressed at various developmental stages of buds,stems,leaves,flowers,and fruits,suggesting that the function of BHLH was associated with the development of different tissues and organs of blueberry,Duke.The present study would provided a foundation for further investigations on the classification and functions of the blueberry BHLH family.展开更多
Osmanthus fragrans is one of the top ten traditional flowers in China.It is divided into three different groups according to its color.α-Carotene and β-carotene are the main determinants to distinguish the color dif...Osmanthus fragrans is one of the top ten traditional flowers in China.It is divided into three different groups according to its color.α-Carotene and β-carotene are the main determinants to distinguish the color differences between three groups.However,the dominant genes and transcription factors involved in carotenoid metabolism remain unclear.CPTA treatment(0.7mmol·L−1)remarkably promoted lycopene,α-carotene and β-carotene contents in flowers.Transcriptome sequencing analysis revealed that CPTA treatment could trigger chain reactions in carotenoid metabolism pathway genes.Four up-regulated and 10 down-regulated transcription factors which have close association with carotenoid variation were significantly induced by CPTA treatment.The up-regulated TFs such as MYB43,MYB123,HSF,were further subjected to transcript expression determination in different cultivars with drastic colors.Among them,transcript expression of four up-regulated TFs coincided with the carotenoid accumulation in different cultivars.We selected up-regulated OfMYB43 to verify its function,which is related to stress tolerance and transcriptional regulation.Transient overexpression of OfMYB43 in O.fragrans flowers showed that it could remarkably promote the expression of PDS,ZISO,LCYE and CCD4,leading to increased accumulation of β-branch carotenoids.OfMYB43 was a potential positive regulator of carotenoid biosynthesis in O.fragrans flowers.This study provides insight into the molecular mechanism of carotenoid metabolism in O.fragrans.展开更多
Transcription factors(TFs)orchestrate the regulation of cellular gene expression and thereby determine cell functionality.In this study,we analyzed the distribution of TFs containing domains,which named as ZnFTFs,both...Transcription factors(TFs)orchestrate the regulation of cellular gene expression and thereby determine cell functionality.In this study,we analyzed the distribution of TFs containing domains,which named as ZnFTFs,both in ascomycete and basidiomycete fungi.We found that ZnFTFs were widely distributed in these fungal species,but there was more expansion of the ZnFTF class in Ascomycota than Basidiomycota.We identified 40 ZnFTFs in Ustilaginoidea virens,and demonstrated the involvement of UvZnFTF1 in vegetative growth,conidiation,pigment biosynthesis and pathogenicity.RNA-Seq analysis suggested that UvZnFTF1 may regulate different nutrient metabolism pathways,the production of secondary metabolites,and the expression of pathogen-host interaction genes and secreted protein-encodi ng genes.Analysis of the distributi on of differe nt fungal TFs in U.virens further dem on strated that UvZnFTFs make up a large TF family and may play essential biological roles in U.virens.展开更多
Anther development is a programmed biological process crucial to plant male reproduction. Genomewide analyses on the functions of transcriptional factor(TF) genes and their microRNA(miRNA) regulators contributing to a...Anther development is a programmed biological process crucial to plant male reproduction. Genomewide analyses on the functions of transcriptional factor(TF) genes and their microRNA(miRNA) regulators contributing to anther development have not been comprehensively performed in maize. Here, using published RNA-Seq and small RNA-Seq(sRNA-Seq) data from maize anthers at ten developmental stages in three genic male-sterility(GMS) mutants(ocl4, mac1, and ms23) and wild type W23, as well as newly sequenced maize anther transcriptomes of ms7-6007 and lob30 GMS mutants and their WT lines, we analyzed and found 1079 stage-differentially expressed(stage-DE) TF genes that can be grouped into six(premeiotic, meiotic, postmeiotic, premeiotic-meiotic, premeiotic-postmeiotic, and meiotic-postmeiotic clusters) expression clusters. Functional enrichment combined with cytological and physiological analyses revealed specific functions of genes in each expression cluster. In addition, 118 stage-DE miRNAs and99 miRNA-TF gene pairs were identified in maize anthers. Further analyses revealed the regulatory roles of zma-miR319 and zma-miR159 as well as ZmMs7 and ZmLOB30 on ZmGAMYB expression. Moreover,ZmGAMYB and its paralog ZmGAMYB-2 were demonstrated as novel maize GMS genes by CRISPR/Cas9 knockout analysis. These results extend our understanding on the functions of miRNA-TF gene regulatory pairs and GMS TF genes contributing to male fertility in plants.展开更多
基金funded by the National Key Research and Development Program of China(2022YFD1201600)the earmarked fund for the China Agriculture Research System(CARS-26)+1 种基金the Fundamental Research Funds for the Central Universities,China(SWU-XDJH202308)the Science and Technology Research Program of Chongqing Municipal Education Commission,China(KJQN202001418)。
文摘One of the main diseases that adversely impacts the global citrus industry is citrus bacterial canker(CBC),caused by the bacteria Xanthomonas citri subsp.citri(Xcc).Response to CBC is a complex process,with both proteinDNA as well as protein–protein interactions for the regulatory network.To detect such interactions in CBC resistant regulation,a citrus high-throughput screening system with 203 CBC-inducible transcription factors(TFs),were developed.Screening the upstream regulators of target by yeast-one hybrid(Y1H)methods was also performed.A regulatory module of CBC resistance was identified based on this system.One TF(CsDOF5.8)was explored due to its interactions with the 1-kb promoter fragment of CsPrx25,a resistant gene of CBC involved in reactive oxygen species(ROS)homeostasis regulation.Electrophoretic mobility shift assay(EMSA),dual-LUC assays,as well as transient overexpression of CsDOF5.8,further validated the interactions and transcriptional regulation.The CsDOF5.8–CsPrx25 promoter interaction revealed a complex pathway that governs the regulation of CBC resistance via H2O2homeostasis.The high-throughput Y1H/Y2H screening system could be an efficient tool for studying regulatory pathways or network of CBC resistance regulation.In addition,it could highlight the potential of these candidate genes as targets for efforts to breed CBC-resistant citrus varieties.
基金supported by the Hebei Grass Industry Innovation Team of the Modern Agricultural Industry Technology System(HBCT2018050204).
文摘Allium senescens,is an important economic and ecological grassland plant with drought-resistant characteristics.A TCP protein transcription factor is important in the regulation of plant development and adverse responses.However,the mechanism by which TCP transcription functions in drought resistance in Allium senescens is still not clear.Here,we obtained a total of 190,305 transcripts with 115,562 single gene clusters based on RNA-Seq sequencing of Allium senescens under drought stress.The total number of bases was 97,195,096 bp,and the average length was 841.06 bp.Furthermore,we found that there were eight genes of the TCP family that showed an upregulated expression trend under drought stress in Allium senescens.We carried out an investigation to determine the evolution and function of the AsTCP family and how they produce an effect in drought resistance.The 14 AsTCP genes were confirmed and divided into class I and class II containing CIN and CYC/TBI subfamilies,respectively.We also found that the expression of AsTCP17 was remarkably upregulated with drought treatment.Besides,the transformation of AsTCP17 in Arabidopsis revealed that the protective enzymes,namely polyphenol oxidase(POD)and superoxide dismutase(SOD),were increased by 0.4 and 0.8 times,respectively.Chlorophyll content was also increased,while the H2O2 and malondialdehyde(MDA)contents were decreased.Staining assays with 3,3′-diaminobenzidine(DAB)also suggested that the AsTCP17 downregulates reactive oxygen species(ROS)accumulation.In addition,overexpression of the AsTCP17 affected the accumulation of drought-related hormones in plants,and the synthesis of ABA.The expression of AtSVP and AtNCED3,related ABA synthesis pathway genes,indicated that the level of expression of AtSVP and AtNCED3 was obviously enhanced,with the overexpression of line 6 showing a 20.6-fold and 7.0-fold increase,respectively.Taken together,our findings systematically analyze the AsTCPs family at the transcriptome expression level in Allium senescens,and we also demonstrated that AsTCP17 protein,as a positive regulator,was involved in drought resistance of Allium senescens.In addition,our research contributes to the comprehensive understanding of the drought stress defense mechanism in herbaceous plants.
基金supported by grants from the National Natural Science Foundation of China(Grant No.32002006)China Postdoctoral Science Foundation(Grant No.2020M680984).
文摘Apple(Malus domestica)fruit generally undergoes a climacteric.During its ripening process,there is a peak in ethylene release and its firmness simultaneously decreases.Although more in-depth research into the mechanism of climacteric-type fruit ripening is being carried out,some aspects remain unclear.In this study,we compared the transcriptomes of 0-Pre and 15-Post(pre-and post-climacteric fruit),and 15-Post and 15-MCP[fruit treated with 1-MCP(1-methylcyclopropene)].Various transcription factors,such as MADS-box,ERF,NAC,Dof and SHF were identified among the DEGs(differential gene expressions).Furthermore,these transcription factors were selected for further validation analysis by qRT-PCR.Moreover,yeast one hybrid(Y1H),β-glucuronidase(GUS)transactivation assay and dual-luciferase reporter assay showed that MdAGL30,MdAGL104,MdERF008,MdNAC71,MdDof1.2,MdHSFB2a and MdHSFB3 bound to MdACS1 promoter and directly regulated its transcription,thereby regulating ethylene biosynthesis in apple fruit.Our results provide useful information and new insights for research on apple fruit ripening.
基金funded by the Start-up Foundation for High Talents of Qingdao Agricultural University(No.665/1120012)the Natural Science Foundation of Shandong Province,China(ZR2019QC017)+4 种基金the National Key Research and Development Program,China(2022YFD2300101-1)the Key Research and Development Program of Shandong Province,China(2021LZGC003 and 2021LZGC026-03)Peanut Seed Industry Project in Shandong Province,China(2022LZGC007)the Science&Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta,China(2022SZX18)the Graduate Student Innovation Program of Qingdao Agricultural University(QNYCX23001).
文摘WRKY transcription factors(TFs)have been identified as important core regulators in the responses of plants to biotic and abiotic stresses.Cultivated peanut(Arachis hypogaea)is an important oil and protein crop.Previous studies have identified hundreds of WRKY TFs in peanut.However,their functions and regulatory networks remain unclear.Simultaneously,the AdWRKY40 TF is involved in drought tolerance in Arachis duranensis and has an orthologous relationship with the AhTWRKY24 TF,which has a homoeologous relationship with AhTWRKY106 TF in A.hypogaea cv.Tifrunner.To reveal how the homoeologous AhTWRKY24 and AhTWRKY106 TFs regulate the downstream genes,DNA affinity purification sequencing(DAP-seq)was performed to detect the binding sites of TFs at the genome-wide level.A total of 3486 downstream genes were identified that were collectively regulated by the AhTWRKY24 and AhTWRKY106 TFs.The results revealed that W-box elements were the binding sites for regulation of the downstream genes by AhTWRKY24 and AhTWRKY106 TFs.A gene ontology enrichment analysis indicated that these downstream genes were enriched in protein modification and reproduction in the biological process.In addition,RNA-seq data showed that the AhTWRKY24 and AhTWRKY106 TFs regulate differentially expressed genes involved in the response to drought stress.The AhTWRKY24 and AhTWRKY106 TFs can specifically regulate downstream genes,and they nearly equal the numbers of downstream genes from the two A.hypogaea cv.Tifrunner subgenomes.These results provide a theoretical basis to study the functions and regulatory networks of AhTWRKY24 and AhTWRKY106 TFs.
基金the National Eye Institute(EY022129 to JLGP30-EY022589 to UCSD)+1 种基金the DOD(W81XWH-12-1-0254 to JLG)an unrestricted grant from Research to Prevent Blindness,Inc
文摘Molecular mechanisms of the Kruppel-like family of transcription factors (KLFs) have been studied more in proliferating cells than in post-mitotic cells such as neurons. We recently found that KLFs regulate intrinsic axon growth ability in central nervous system (CNS) neurons in- cluding retinal ganglion cells, and hippocampal and cortical neurons. With at least 15 of 17 KLF family members expressed in neurons and at least 5 structurally unique subfamilies, it is import- ant to determine how this complex family functions in neurons to regulate the intricate genetic programs of axon growth and regeneration. By characterizing the molecular mechanisms of the KLF family in the nervous system, including binding partners and gene targets, and comparing them to defined mechanisms defined outside the nervous system, we may better understand how KLFs regulate neurite growth and axon regeneration.
基金supported by the Natural Science Foundation of Hebei(Grant No.C2021209005)National Natural Science Foundation of China(Grant No.32172583)+1 种基金the Natural Science Foundation for Distinguished Young Scholar of Hebei Province(Grant No.C2022209010)the China Postdoctoral Science Foundation(Grant Nos.2020M673188,2021T140097).
文摘Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species.Whole-genome duplication(WGD)was the dominant event type in almost all Cucurbitaceae plants.The TF families were divided into 1210 orthogroups(OGs),of which,112 were unique to Cucurbitaceae.Although the loss of several gene families was detected in Cucurbitaceae,the gene families expanded in five species that experienced a WGD event comparing with grape.Our findings revealed that the recent WGD events that had occurred in Cucurbitaceae played important roles in the expansion of most TF families.The functional enrichment analysis of the genes that significantly expanded or contracted uncovered five gene families,AUX/IAA,NAC,NBS,HB,and NF-YB.Finally,we conducted a comprehensive analysis of the TCP gene family and identified 16 tendril-related(TEN)genes in 11 Cucurbitaceae species.Interestingly,the characteristic sequence changed from CNNFYFP to CNNFYLP in the TEN gene(Bhi06M000087)of Benincasa hispida.Furthermore,we identified a new characteristic sequence,YNN,which could be used for TEN gene exploitation in Cucurbitaceae.In conclusion,this study will serve as a reference for studying the relationship between gene family evolution and genome duplication.Moreover,it will provide rich genetic resources for functional Cucurbitaceae studies in the future.
基金Supported by (in part) Novartis Pharma GmbH,Germany,BU Transplantation and Immunology (to Lehner F)the Lower Saxony Ministry of Culture and Sciences and the Volk-swagen foundation,Germany,Grant No.25A.5-7251-99-3/00
文摘AIM: To investigate the gene expression pattern of hepatocyte nuclear factor 6 (HNF6) and other liverenriched transcription factors in various segments of the human intestine to better understand the differentiation of the gut epithelium. METHODS: Samples of healthy duodenum and jejunum were obtained from patients with pancreatic cancer whereas ileum and colon was obtained from patients undergoing right or left hemicolectomy or (recto)sigmoid or rectal resection. All surgical specimens were subjected to histopathology. Excised tissue was shock-frozen and analyzed for gene expression of liver-enriched transcription factors by semiquantitative reverse transcription polymerase chain and compared to the human colon carcinoma cell line Caco-2. Protein expression of major liver-enriched transcription factors was determined by Western blotting while the DNA binding of HNF6 was investigated by electromobility shift assays. RESULTS: The gene expression patterning of liverenriched transcription factors differed in the various segments of the human intestine with HNF6 gene expression being most abundant in the duodenum (P < 0.05) whereas expression of the zinc finger protein GATA4 and of the HNF6 target gene ALDH3A1 was most abundant in the jejunum (P < 0.05). Likewise, expression of FOXA2 and the splice variants 2 and 4 of HNF4α were most abundantly expressed in the jejunum (P < 0.05). Essentially, expression of transcription factors declined from the duodenum towards the colon with the most abundant expression in the jejunum and less in the ileum. The expression of HNF6 and of genes targeted by this factor, i.e. neurogenin 3 (NGN3) was most abundant in the jejunum followed by the ileum and the colon while DNA binding activity of HNF4α and of NGN3 was conf irmed by electromobility shift assays to an optimized probe. Furthermore, Western blotting provided evidence of the expression of several liver-enriched transcription factors in cultures of colon epithelial cells, albeit at different levels. CONCLUSION: We describe significant local and segmental differences in the expression of liver-enriched transcription factors in the human intestine which impact epithelial cell biology of the gut.
基金Supported by Ministry of Education,Science and Technological Development of the Republic of Serbia,No.451-03-9/2021-14/200042。
文摘Glioblastoma(GBM)is the most common,most aggressive and deadliest brain tumor.Recently,remarkable progress has been made towards understanding the cellular and molecular biology of gliomas.GBM tumor initiation,progression and relapse as well as resistance to treatments are associated with glioma stem cells(GSCs).GSCs exhibit a high proliferation rate and self-renewal capacity and the ability to differentiate into diverse cell types,generating a range of distinct cell types within the tumor,leading to cellular heterogeneity.GBM tumors may contain different subsets of GSCs,and some of them may adopt a quiescent state that protects them against chemotherapy and radiotherapy.GSCs enriched in recurrent gliomas acquire more aggressive and therapy-resistant properties,making them more malignant,able to rapidly spread.The impact of SOX transcription factors(TFs)on brain tumors has been extensively studied in the last decade.Almost all SOX genes are expressed in GBM,and their expression levels are associated with patient prognosis and survival.Numerous SOX TFs are involved in the maintenance of the stemness of GSCs or play a role in the initiation of GSC differentiation.The fine-tuning of SOX gene expression levels controls the balance between cell stemness and differentiation.Therefore,innovative therapies targeting SOX TFs are emerging as promising tools for combatting GBM.Combatting GBM has been a demanding and challenging goal for decades.The current therapeutic strategies have not yet provided a cure for GBM and have only resulted in a slight improvement in patient survival.Novel approaches will require the fine adjustment of multimodal therapeutic strategies that simultaneously target numerous hallmarks of cancer cells to win the battle against GBM.
基金the National Key Basic Research Project of China(2004CB117503)
文摘This study was conducted to determine the effects of varying the ratio of lysine to digestible energy level On the activity and gene expression of the transcription factors peroxisome proliferator-activated receptor-γ (PPAR-γ) and CCAAT/enhancer-binding protein-or and -β (C/EBP-α and C/EBP-β) to better understand the regulatory mechanisms controlling adipogenesis in fat and muscle tissue of the Rongchang pig. A total of 144 castrated Rongchang pigs weighing approximately 20 kg were used in a 2 ×2 factorial design experiment. Diets were formulated to contain a high (14.22 MJ/kg) or low (13.11 MJ/kg) digesti- ble energy (DE) level. Within each energy level, pigs were fed diets containing a high lysine: DE ratio (0.67,0. 53, or 0. 42) or a low lysine : DE ratio (0.49,0.38 ,or 0.30) during the periods from 20 to 50 kg, 50 to 80 kg, and 80 kg to slaughter, respectively. Each diet was fed to six replicate pens, each containing nine pigs. When the pigs reached average live weights of 20,35,60, and 90 kg ,one pig from each of the replicates was chosen at random and slaughtered.Samples of back fat and longissimus dorsi muscle were collected for the assessment of transcriptional factor. The results showed that feeding a high DE level significantly increased ( P 〈 0.05 ) the expression of PPAR-T at 60 and 90 kg in muscle and at 35,60, and 90 kg in back fat. Energy level also significantly increased the expression of C/EBP-fl at 35 and 60 kg in both muscle and back fat ( P 〈 0.05 ). Higher dieta- ry lysine increased the expression of C/EBP-fl in muscle at 35 and 90 kg ( P 〈 0.05), but decreased the expression in back fat at 35 (P = 0.03 ) and 90 kg (P = 0.09). The lysine level increased the expression of PPAR-3~ in muscle at 60 kg only. Energy level and lysine content had no significant effects on promote the activity of PPAR-γ, C/EBP-α, or C/EBP-β either in muscle or in back fat at any level of the body weights tested. Collectively, these data indicated that dietary energy density and lysine level were equally important for lipid deposition in muscle tissue, whereas dietary energy density was more important than lysine level for fat deposition in fat tissue.
基金supported by Storrs Agricultural Experiment Station Hatch Project CONS00844(KEG)
文摘Background: The use of equine bone marrow mesenchymal stem cells (BMSC) is a novel method to improve fracture healing in horses. However, additional research is needed to identify optimal culture conditions and to determine the mechanisms involved in regulating BMSC differentiation into osteoblasts. The objectives of the experiments were to determine: 1) if autologous or commercial serum is better for proliferation and differentiation of equine BMSC into osteoblasts, and 2) the expression of key transcription factors during the differentiation of equine BMSC into osteoblasts. Equine BMSC were isolated from the sterna of 3 horses, treated with purchased fetal bovine serum (FBS) or autologous horse serum (HS), and cell proliferation determined. To induce osteoblast differentiation, cells were incubated with L-ascorbic acid-2-phosphate and glycerol-2-phosphate in the presence or absence of human bone morphogenetic protein2 (BMP2), dexamethasone (DEX), or combination of the two. Alkaline phosphatase (ALP) activity, a marker of osteoblast differentiation, was determined by ELISA. Total RNA was isolated from differentiating BMSC between d 0 to 18 to determine expression of runt-reloted tronscrJption foctor2 (Runx2), osterix (Osx), and T-box3 (Tbx3). Data were analyzed by ANOVA. Results: Relative to control, FBS and HS increased cell number (133 ± 5 and 116 ± 5%, respectively; P 〈 0.001) and 5-bromo- 2'-deoxyuridine (BrdU) incorporation (167 ± 6 and 120 ± 6%, respectively; P 〈 0.001). Treatment with DEX increased ALP activity compared with control (1,638 ± 38%; P 〈 0.001). In the absence and presence of Dex, BMP-2 did not alter ALP activity (P 〉 0.8). Runt-reloted transcription foctor2 expression increased 3-fold (P 〈 0.001) by d 6 of culture. Osterix expression increased 94old (P 〈 0.05) by d 18 of culture. Expression of Tbx3 increased 1.8-fold at d 3 (P 〈 0.01); however expression was reduced 4-fold at d 18 (P 〈 0.01). Conclusions: Dexamethasone, but not BMP-2, is required for differentiation of equine BMSC into osteoblasts. In addition, expression of Runx2 and osterix increased and expression of Tbx3 is reduced during differentiation.
基金Supported by National Natural Science Foundation of China(No.81470614,No.81460163,No.81300786)Fundamental Research Funds for the Central Universities(No.xjj2014146)+1 种基金Specialized Research Fund for the Doctoral Program of Higher Education(No.20133601120012)Key International Communication Project of Shaanxi province(No.2012KW-31)
文摘AIMTo investigate the expression of transcription factors Slug in human lens epithelial cells (HLECs) undergoing epithelial-mesenchymal transition (EMT) induced by connective tissue growth factor (CTGF).METHODSHLECs were treated with CTGF of different concentrations (20, 50 and 100 ng/mL) or without CTGF (control) for 24h. The morphological changes of HLECs were analysed by microscopy. The expression and cellular localization of Slug was evaluated by immumo-fluorescence. Expressions of Slug, E-cadherin and alpha smooth muscle actin (α-SMA) were further determined by Western blot analysis.RESULTSHLECs showed spidle fibrolasts-like characteristics and loosely connected each other after CTGF treatment. The immuno-fluorescence staining indicated that Slug was localized in the nuclei and its expression was induced by CTGF. The relative expressions of Slug protein were 1.64±0.11, 1.96 ±0.03, 3.12 ±0.10, and 4.08±0.14, respectively, in response to control group and treatment with CTGF of 20, 50 and 100 ng/mL (F=443.86, P<0.01). The increased Slug protein levels were correlated well with up-expression of α-SMA (0.78±0.05, 0.85±0.06, 2.17±0.15, 2.86±0.10; F=449.85, P<0.01) and down-expression of E-cadherin (2.50±0.11, 1.79±0.26, 1.05±0.14, 0.63±0.08; F=101.55, P<0.01).CONCLUSIONTranscription factor Slug may be involved in EMT of HLECs induced by CTGF in vitro.
基金Supported by Houston Methodist Cancer Center Innovation Award。
文摘Specificity protein(Sp)transcription factors(TFs)Sp1,Sp3 and Sp4,and the orphan nuclear receptor 4A1(NR4A1)are highly expressed in pancreatic tumors and Sp1 is a negative prognostic factor for pancreatic cancer patient survival.Results of knockdown and overexpression of Sp1,Sp3 and Sp4 in pancreatic and other cancer lines show that these TFs are individually pro-oncogenic factors and loss of one Sp TF is not compensated by other members.NR4A1 is also a prooncogenic factor and both NR4A1 and Sp TFs exhibit similar functions in pancreatic cancer cells and regulate cell growth,survival,migration and invasion.There is also evidence that Sp TFs and NR4A1 regulate some of the same genes including survivin,epidermal growth factor receptor,PAX3-FOXO1,α5-andα6-integrins,β1-,β3-andβ4-integrins;this is due to NR4A1 acting as a cofactor and mediating NR4A1/Sp1/4-regulated gene expression through GC-rich gene promoter sites.Several studies show that drugs targeting Sp downregulation or NR4A1 antagonists are highly effective inhibitors of Sp/NR4A1-regulated pathways and genes in pancreatic and other cancer cells,and the triterpenoid celastrol is a novel dual-acting agent that targets both Sp TFs and NR4A1.
文摘Larix olgensis A.Henry is a fast-growing tree used for aff orestation in northeastern China and has great ecological and economic value.For studying developmental genes in the xylem of this species,we investigated the Myb transcription factor family,one of the largest families of transcription factors in plants,which plays an important role in the regulation of lignifi cation in plant secondary walls.By sequencing a L.olgensis cDNA library using the Illumina HiSeq2500 high-throughput sequencing platform,we obtained 58,683 unigene sequences,of which 16,554 unigenes were longer than 1000 bp,accounting for 28.2%of the total database.The alignment of these genes with the GO,COG,KEGG,Swiss-Prot and NR databases resulted in annotated 29,350 unigenes.We obtained a total of 1460 differentially expressed genes,of which 453 were upregulated and 1007 were downregulated at the two developmental stages analyzed.The gene annotations showed a wide range of biological functions and metabolic pathways.The 10 Myb transcription factors that were obtained from the diff erentially expressed genes were analyzed by real-time quantitative PCR(qRT-PCR).The results showed that four Myb transcription factors may be associated with xylem development in L.olgensis.Due to the large genome size of conifers,genomics research on these species has lagged behind that for other plant groups.Our data provide the basis for further studies on xylem development in L.olgensis.
基金Research in the Mu lab is supported by grants from the National Eye Institute(EY020545)the SUNY/RF Research Collaboration Fundan unrestricted grant from Research to Prevent Blindness
文摘The retina and its development: The retina is an essential part of the visual system. A myriad of eye diseases are characterized by retinal degeneration, caused by either genetic or environmental factors. This underscores the importance of studying the genetic and molecular mechanisms that regulate the generation and maintenance of neurons in the mammalian retina. Our recent studies demonstrate that two related transcription factors Onecutl (Ocl) and Onecut2 (0c2) regulate multiple cell fates in the mouse retina, and their absence results in progressive retinal neurodegeneration (Wu et al., 2012, 2013; Sapkota et al., 2014).
基金supported by grants from the Canada Research Chairs programthe NSERC Engage and Engage Plus program
文摘Diseases and disorders of the central nervous system often require significant interventions to restore lost function due to their com- plexity. Examples of such disorders include Parkinson's disease, Alzheimer's disease, multiple sclerosis, traumatic brain injury, and spinal cord in)ury. These diseases and disorders result trom healthy cells being destroyed, which in turn causes dysfunction in the cen- tral nervous system, The death of these cells can trigger a cascade of events that affect the rest of the body, causing symptoms that become progressively worse over time. Developing strategies for repairing the damage to the central nervous system remains chal- lenging, in part due to its inability to regenerate.
文摘Background/Aim: MicroRNAs with regulatory functions in gene expression are implicated in different diseases. The present study investigated differentially expressed miRNAs that possibly influence transcription factors involved in insulin gene expression in Chronic Pancreatitis (CP) employing bioinformatics approaches. Methods: Pancreatic tissues were collected from CP patients undergoing partial pancreatectomy (n = 16) and controls (n = 15) undergoing resections for non-pancreatic malignancies. MiRNA profiles obtained using microarrays were validated by qRT-PCR. Target search involving miRWalk and TarBase as well as functional annotation employing KEGG (Kyoto encyclopedia of genes and genomes) and DAVID (Database for Annotation) databases were performed. Ingenuity pathway analysis (IPA) was used to construct networks relating miRNAs to their target genes. mRNA and proteins related to insulin gene transcription factors and hormones were evaluated by qRT-PCR and western blotting followed by confirmation upon immunofluorescent staining. Results: Microarray data revealed 10 up-regulated and 15 down-regulated miRNAs in CP as compared to controls (Log2 FC > 2). Bioinformatic analysis showed 8399 target genes and KEGG pathway analysis suggested a role for the dysregulated miRNAs in modulating cytokine signaling, fibrosis, JAK-STAT signaling and insulin synthesis. IPA analysis suggested a simplified network attributing dysregulated miRNAs to NFκB-dependent cytokine signaling. Further, associations could be noted between miRNA 200b with Maf A, 138-1 with Neuro D and 27b with FoxO1. Decreases in mRNA levels of Pdx1, Neuro D and increases of Maf A and FoxO1 transcription factors could be noted (P Conclusion: Our results identified dysregulation of miRNAs 138-1, 27b and 200b which were found to be associated with insulin gene transcription factors Neuro D, FoxO1 and Maf A respectively.
基金supported by the National Natural Science Foundation of China (31301754)the Chinese Academy of Agricultural Sciences-Agricultural Science and Technology Innovation Program (CAAS-ASTIP)the Cultivation Plan for Youth Agricultural Science and Technology Innovative Talents of Liaoning Province, China (2015059)
文摘The highbush blueberry(Vaccinium corymbosum),Duke,was used to construct a de novo transcriptome sequence library and to perform data statistical analysis.Mega 4,CLC Sequence Viewer 6 software,and quantitative PCR were employed for bioinformatics and expression analyses of the basic helix-loop-helix(BHLH)transcription factors of the sequencing library.The results showed that 28.38 gigabytes of valid data were obtained from transcriptome sequencing and were assembled into 108 033 unigenes.Functional annotation showed that 32 244 unigenes were annotated into Clusters of Orthologous Groups(COG)and Gene Ontology(GO)databases,whereas the rest of the 75 789 unigenes had no matching information.By using COG and GO classification tools,sequences with annotation information were divided into 25 and 52 categories,respectively,which involved transport and metabolism,transcriptional regulation,and signal transduction.Analysis of the transcriptome library identified a total of 59 BHLH genes.Sequence analysis revealed that 55 genes of that contained a complete BHLH domain.Furthermore,phylogenetic analysis showed that BHLH genes of blueberry(Duke)could be divided into 13 sub-groups.PCR results showed that 45 genes were expressed at various developmental stages of buds,stems,leaves,flowers,and fruits,suggesting that the function of BHLH was associated with the development of different tissues and organs of blueberry,Duke.The present study would provided a foundation for further investigations on the classification and functions of the blueberry BHLH family.
基金supported by the Fundamental Research Fund for the Central Universities(Grant No.2013PY088).
文摘Osmanthus fragrans is one of the top ten traditional flowers in China.It is divided into three different groups according to its color.α-Carotene and β-carotene are the main determinants to distinguish the color differences between three groups.However,the dominant genes and transcription factors involved in carotenoid metabolism remain unclear.CPTA treatment(0.7mmol·L−1)remarkably promoted lycopene,α-carotene and β-carotene contents in flowers.Transcriptome sequencing analysis revealed that CPTA treatment could trigger chain reactions in carotenoid metabolism pathway genes.Four up-regulated and 10 down-regulated transcription factors which have close association with carotenoid variation were significantly induced by CPTA treatment.The up-regulated TFs such as MYB43,MYB123,HSF,were further subjected to transcript expression determination in different cultivars with drastic colors.Among them,transcript expression of four up-regulated TFs coincided with the carotenoid accumulation in different cultivars.We selected up-regulated OfMYB43 to verify its function,which is related to stress tolerance and transcriptional regulation.Transient overexpression of OfMYB43 in O.fragrans flowers showed that it could remarkably promote the expression of PDS,ZISO,LCYE and CCD4,leading to increased accumulation of β-branch carotenoids.OfMYB43 was a potential positive regulator of carotenoid biosynthesis in O.fragrans flowers.This study provides insight into the molecular mechanism of carotenoid metabolism in O.fragrans.
基金supported by the National Natural Science Foundation of China(Grant No.31601593)the Young Elite Scientist Sponsorship of China Association for Science and Technology(Grant No.YESS20170108)the Natural Science Foundation of Jiangsu Province,China(Grant No.BK20160588).
文摘Transcription factors(TFs)orchestrate the regulation of cellular gene expression and thereby determine cell functionality.In this study,we analyzed the distribution of TFs containing domains,which named as ZnFTFs,both in ascomycete and basidiomycete fungi.We found that ZnFTFs were widely distributed in these fungal species,but there was more expansion of the ZnFTF class in Ascomycota than Basidiomycota.We identified 40 ZnFTFs in Ustilaginoidea virens,and demonstrated the involvement of UvZnFTF1 in vegetative growth,conidiation,pigment biosynthesis and pathogenicity.RNA-Seq analysis suggested that UvZnFTF1 may regulate different nutrient metabolism pathways,the production of secondary metabolites,and the expression of pathogen-host interaction genes and secreted protein-encodi ng genes.Analysis of the distributi on of differe nt fungal TFs in U.virens further dem on strated that UvZnFTFs make up a large TF family and may play essential biological roles in U.virens.
基金funded by the National Natural Science Foundation of China (31771875, 31971958, and 31871702)the Fundamental Research Funds for the Central Universities of China (2302019FRF-TP-19-013A1, 06500136)the National Key Research and Development Program of China (2017YFD0102001, 2018YFD0100806, and 2017YFD0101201)。
文摘Anther development is a programmed biological process crucial to plant male reproduction. Genomewide analyses on the functions of transcriptional factor(TF) genes and their microRNA(miRNA) regulators contributing to anther development have not been comprehensively performed in maize. Here, using published RNA-Seq and small RNA-Seq(sRNA-Seq) data from maize anthers at ten developmental stages in three genic male-sterility(GMS) mutants(ocl4, mac1, and ms23) and wild type W23, as well as newly sequenced maize anther transcriptomes of ms7-6007 and lob30 GMS mutants and their WT lines, we analyzed and found 1079 stage-differentially expressed(stage-DE) TF genes that can be grouped into six(premeiotic, meiotic, postmeiotic, premeiotic-meiotic, premeiotic-postmeiotic, and meiotic-postmeiotic clusters) expression clusters. Functional enrichment combined with cytological and physiological analyses revealed specific functions of genes in each expression cluster. In addition, 118 stage-DE miRNAs and99 miRNA-TF gene pairs were identified in maize anthers. Further analyses revealed the regulatory roles of zma-miR319 and zma-miR159 as well as ZmMs7 and ZmLOB30 on ZmGAMYB expression. Moreover,ZmGAMYB and its paralog ZmGAMYB-2 were demonstrated as novel maize GMS genes by CRISPR/Cas9 knockout analysis. These results extend our understanding on the functions of miRNA-TF gene regulatory pairs and GMS TF genes contributing to male fertility in plants.