Isolation and Characterization of a C-repeat Binding Transcription Factor from Maize

C-repeat binding proteins （CBFs） are a group of transcription factors that have been proven to be important for stress tolerance in plants. Many of these transcription factors transactivate the promoters of cold-regulated genes via binding to low temperature-or dehydration-responsive c/s-elements, thus conferring plants cold acclimation. In the present study, we isolated a C-repeat binding transcription factor from maize using the yeast one-hybrid system with the C-repeat motif from the promoter of the Arabidopsis COR15a gene as bait. The isolated transcription factor is highly similar to the Arabidopsis CBF3 in their predicted amino acid sequences, and is therefore designated ZmCBF3. Point mutation analyses of the ZmCBF3-binding c/s-element revealed （A/G）（C/T）CGAC as the core binding sequence. Expression analyses showed that ZmCBF3 was upregulated by both abscisic acid and low temperature, and was actively expressed during embryogenesis, suggesting that ZmCBF3 plays a role in stress response in maize.

Identifying changes in punitive transcriptional factor binding sites from regulatory single nucleotide polymorphisms that are significantly associated with disease or sickness

AIM To identify punitive transcriptional factor binding sites(TFBS) from regulatory single nucleotide polymorphisms(rS NPs) that are significantly associated with disease.METHODS The genome-wide association studies have provided us with nearly 6500 disease or trait-predisposing SNPs where 93% are located within non-coding regions such as gene regulatory or intergenic areas of the genome. In the regulatory region of a gene, a SNP can change the DNA sequence of a transcriptional factor(TF) motif and in turn may affect the process of gene regulation. SNP changes that affect gene expression and impact gene regulatory sequences such as promoters, enhancers, and silencers are known as rS NPs. Computational tools can be used to identify unique punitive TFBS created by rS NPs that are associated with disease or sickness. Computational analysis was used to identify punitive TFBS generated by the alleles of these rS NPs.RESULTS r SNPs within nine genes that have been significantly associated with disease or sickness were used to illustrate the tremendous diversity of punitive unique TFBS that can be generated by their alleles. The genes studied are the adrenergic, beta, receptor kinase 1, the v-akt murine thymoma viral oncogene homolog 3, the activating transcription factor 3, the type 2 demodkinase gene, the endothetal Per-Arnt-Sim domain protein 1, the lysosomal acid lipase A, the signal Transducer and Activator of Transcription 4, the thromboxane A2 receptor and the vascular endothelial growth factor A. From this sampling of SNPs among the nine genes, there are 73 potential unique TFBS generated by the common alleles comparedto 124 generated by the minor alleles indicating the tremendous diversity of potential TFs that are capable of regulating these genes.CONCLUSION From the diversity of unique punitive binding sites for TFs, it was found that some TFs play a role in the disease or sickness being studied.

A distribution pattern assisted method of transcription factor binding site discovery for both yeast and filamentous fungi

Transcription factors (TFs) are the core sentinels of gene regulation functioning by binding to highly specific DNA sequences to activate or repress the recruitment of RNA polymerase. The ability to identify transcription factor binding sites (TFBSs) is necessary to understand gene regulation and infer regulatory networks. Despite the fact that bioinformatics tools have been developed for years to improve computational identification of TFBSs, the accurate prediction still remains changeling as DNA motifs recognized by TFs are typically short and often lack obvious patterns. In this study we introduced a new attribute-motif distribution pattern (MDP) to assist in TFBS prediction. MDP was developed using a TF distribution pattern curve generated by analyzing 25 yeast TFs and 37 of their experimentally validated binding motifs, followed by calculating a scoring value to quantify the reliability of each motif prediction. Finally, MDP was tested using another set of 7 TFs with known binding sites to in silico validate the approach. The method was further tested in a non-yeast system using the filamentous fungus Magnaporthe oryzae transcription factor MoCRZ1. We demonstrate superior prediction reranking results using MDP over the commonly used program MEME and the other four predictors. The data showed significant improvements in the ranking of validated TFBS and provides a more sensitive statistics based approach for motif discovery.

Bioinformatic screening of the binding transcription sites in the regulatory regions of genes up-regulated in response to oxidative stress

This study focuses on bioinformatics search for new regulatory structures in the non-coding DNA, located around the patterns of gene expression levels changed significantly in response to oxidative stress. Hypothesized that all of the genes increase the expression in response to oxidative stress may have the same motifs in non-coding DNA. To search for motifs created an integrated collection database of transcription binding sites - JASPAR, TRANSFAC, Hocomoco TF Homo sapiens, Uniprobe TF Mus musculus. Two types of regulatory regions: the promoter region and the sequence with the capture of potential cis-regulatory modules. In the regulatory regions of genes increase the expression in response to oxidative stress, in contrast to the gene expression level did not change, families of transcription factors identified SOX (1-30) and HX (A, B, C, D).

A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas

Identification of genetic signatures is the main objective for many computational oncology studies. The signature usually consists of numerous genes that are differentially expressed between two clinically distinct groups of samples, such as tumor subtypes. Prospectively, many signatures have been found to generalize poorly to other datasets and, thus, have rarely been accepted into clinical use. Recognizing the limited success of traditionally generated signatures, we developed a systems biology-based framework for robust identification of key transcription factors and their genomic regulatory neighborhoods. Application of the framework to study the differences between gastrointestinal stromal tumor (GIST) and leiomyosarcoma (LMS) resulted in the identification of nine transcription factors (SRF, NKX2-5, CCDC6, LEF1, VDR, ZNF250, TRIM63, MAF, and MYC). Functional annotations of the obtained neighborhoods identified the biological processes which the key transcription factors regulate differently between the tumor types. Analyzing the differences in the expression patterns using our approach resulted in a more robust genetic signature and more biological insight into the diseases compared to a traditional genetic signature.

Overexpression of GATA binding protein 4 and myocyte enhancer factor 2C induces differentiation of mesenchymal stem cells into cardiac-like cells

BACKGROUND Heart diseases are the primary cause of death all over the world.Following myocardial infarction,billions of cells die,resulting in a huge loss of cardiac function.Stem cell-based therapies have appeared as a new area to support heart regeneration.The transcription factors GATA binding protein 4(GATA-4)and myocyte enhancer factor 2C(MEF2C)are considered prominent factors in the development of the cardiovascular system.AIM To explore the potential of GATA-4 and MEF2C for the cardiac differentiation of human umbilical cord mesenchymal stem cells(hUC-MSCs).METHODS hUC-MSCs were characterized morphologically and immunologically by the presence of specific markers of MSCs via immunocytochemistry and flow cytometry,and by their potential to differentiate into osteocytes and adipocytes.hUC-MSCs were transfected with GATA-4,MEF2C,and their combination to direct the differentiation.Cardiac differentiation was confirmed by semiquant itative real-time polymerase chain reaction and immunocytochemistry.RESULTS hUC-MSCs expressed specific cell surface markers CD105,CD90,CD44,and vimentin but lack the expression of CD45.The transcription factors GATA-4 and MEF2C,and their combination induced differentiation in hUC-MSCs with significant expression of cardiac genes i.e.,GATA-4,MEF2C,NK2 homeobox 5(NKX2.5),MHC,and connexin-43,and cardiac proteins GATA-4,NKX2.5,cardiac troponin T,and connexin-43.CONCLUSION Transfection with GATA-4,MEF2C,and their combination effectively induces cardiac differentiation in hUC-MSCs.These genetically modified MSCs could be a promising treatment option for heart diseases in the future.

Maintaining cholesterol homeostasis: Sterol regulatory element-binding proteins

The molecular mechanism of how hepatocytes maintain cholesterol homeostasis has become much more transparent with the discovery of sterol regulatory element binding proteins (SREBPs) in recent years. These membrane proteins aremembers of the basic helix-loop-helix-leucine zipper (bHLHZip) family of transcription factors. They activate the expression of at least 30 genes involved in the synthesis of cholesterol and lipids. SREBPs are synthesized as precursor proteins in the endoplasmic reticulum (ER), where they form a complex with another protein, SREBP cleavage activating protein (SCAP). The SCAP molecule contains a sterol sensory domain. In the presence of high cellular sterol concentrations SCAP confines SREBP to the ER. With low cellular concentrations, SCAP escorts SREBP to activation in the Golgi. There, SREBP undergoes two proteolytic cleavage steps to release the mature, biologically active transcription factor, nuclear SREBP (nSREBP). nSREBP translocates to the nucleus and binds to sterol response elements (SRE) in the promoter/enhancer regions of target genes. Additional transcription factors are required to activate transcription of these genes. Three different SREBPs are known, SREBPs-1a, -1c and -2. SREBP-1a and -1c are isoforms produced from a single gene by alternate splicing. SREBP-2 is encoded by a different gene and does not display any isoforms. It appears that SREBPs alone, in the sequence described above, can exert complete control over cholesterol synthesis, whereas many additional factors (hormones, cytokines, etc.) are required for complete control of lipid metabolism. Medicinal manipulation of the SREBP/SCAP system is expected to prove highly beneficial in the management of cholesterol-related disease.

Role of the PEST sequence in the long-type GATA-6 DNA-binding protein expressed in human cancer cell lines

GATA-6 mRNA utilizes two Met-codons in frame as translational initiation codons in cultured mammalian cells. Deletion of the nucleotide sequence encoding the PEST sequence between the two initiation codons unusually reduced the protein molecular size on SDS-polyacrylamide gel-electrophoresis. The reduced molecular size is ascribed to the molecular property of GATA-6, since both amino-and carboxy-lterminal tags introduced into GATA-6 were detected on the gel. This PEST sequence seems to contribute to expansion of the long-type GATA-6 molecule. The long-type GATA-6 containing the PEST sequence exhibits more activation potential than that without this sequence, the latter’s activity being similar to that of the short-type GATA-6. We further demonstrated that human colon and lung cancer cell lines express both the long-type GATA-6 and the short-type GATA-6 in their nuclei.

低浓度氟化钠对人牙髓细胞的成骨/成牙本质分化的影响

目的探讨低浓度氟化钠对人牙髓细胞(human dental pulp cells,hDPCs)成骨/成牙本质分化的影响。方法本研究已通过单位伦理委员会审查批准。原代培养hDPCs,采用MTT法检测不同浓度氟化钠对hDPCs增殖的影响;选取合适浓度的氟化钠加入成骨/成牙本质分化诱导培养液中,对hDPCs进行体外诱导,通过茜素红染色检测hDPCs成骨/成牙本质分化能力的变化,RT⁃qPCR检测分化相关基因的mRNA表达;同时通过RT⁃qPCR和Western blot检测hDPCs成骨/成牙本质分化过程中内质网应激相关基因的表达。结果低浓度氟化钠(0.1 mmol/L)在体外可刺激hDPCs增殖,高浓度氟化钠(5~10 mmol/L)可抑制hDPCs增殖(P<0.05)。选取0.1 mmol/L氟化钠体外混合成骨/成牙本质分化诱导培养后hDPCs的茜素红染色增加,成骨/成牙本质分化相关基因牙本质涎磷蛋白(dentin sialophosphoprotein,DSPP)、骨涎蛋白(bone sialoprotein,BSP)和骨钙蛋白(osteocalcin,OCN)mRNA表达水平升高(P<0.05)。同时在此过程中RT⁃qPCR检测出mRNA水平hDPCs内质网应激相关基因:剪切x盒结合蛋白1(splicing x⁃box binding protein⁃1,sXBP1)、葡萄糖调节蛋白78(glucose⁃regulated protein 78,GRP78)以及活化转录因子4(activating transcription factor 4,ATF4)表达升高(P<0.05);Western blot检测出氟化钠混合成骨/成牙本质分化培养后细胞磷酸化真核起始因子⁃2α(phosphorylated eukary⁃otic initiation factor⁃2α,p⁃eIF2α)、磷酸化蛋白激酶样内质网激酶(phosphorylated the RNA⁃activated protein kinase⁃like ER⁃resident kinase,p⁃PERK)和ATF4蛋白表达增加(P<0.05)。结论低剂量氟化钠促进人牙髓细胞的成骨/成牙本质分化并伴有内质网应激水平的升高。

Isolation of cDNAs Enconding Two Distinct Transcription Factors Binding to DRE cis-acting Element Involved in Cold-and drought-induced Expression of Arabidopsis rd29A Gene

Previous study has defined DRE (dehydration responsive element) cis acting element and its important role in expressions of Arabidopsis rd29A gene under cold, dehydration and high salt stresses. In order to clarify the expression mechanism of rd29A gene, we isolated two cDNA clones that encoded DRE binding proteins ( DREB1 and DREB2 ) from cold and drought treated Arabidopsis plants, using DRE cis acting element in the promoter region of rd29A gene and yeast One Hybrid screening method. Experiments showed both DREB1 and DREB2 specifically interacted with DRE cis element. Homologous analysis showed no significant similarity between DREB1 and DREB2 in whole deduced amino acid sequences. However, both DREB1 and DREB2 proteins contained a conserved DNA binding domain (AP2/EREBP domain). Structural analysis of proteins also showed they had a nuclear localization signal (NLS) in their N terminal region and an acidic activation region in their C terminal region. AP2/EREBP domain is composed of 58 amino acids, which presents in a large family of plant genes encoding DNA binding proteins. We analyzed many plant transcription factors containing conserved AP2/EREBP domains. The 14th valine (V) and 19th glutamate (E) in the amino acid sequence of AP2/EREBP domains might be the consensus recognizing and binding to DRE cis element. Northern analysis indicated that DREB1 gene was induced by low temperature, whereas DREB2 gene was induced by dehydration and high salt stresses. Present studies suggest that the expression of rd29A gene under low temperature, dehydration and high salt stresses is regulated by DREB1 and DREB2 transcriptional factors in two separate signal transduction pathways, respectively.

联合检测外周血TIRAP、FOXO3a、HBP预测脓毒症患者近期预后的价值及意义

目的探讨联合检测外周血TOLL/白介素-1受体相关蛋白(TIRAP)、叉头蛋白转录因子3a(FOXO3a)、肝素结合蛋白(HBP)对脓毒症患者近期预后的预测价值。方法回顾性收集2020年1月—2022年12月本院205例脓毒症患者的临床资料,根据28 d生存情况分为生存组157例、死亡组48例。统计两组外周血TIRAP、FOXO3a、HBP及急性生理功能和慢性健康状况评分系统Ⅱ(APACHEⅡ)、序贯器官衰竭评估(SOFA)评分。分析TIRAP、FOXO3a、HBP与APACHEⅡ、SOFA评分的相关性。采用Logistic回归方程分析TIRAP、FOXO3a、HBP交互作用对脓毒症近期预后的影响。评价TIRAP、FOXO3a、HBP联合预测脓毒症近期预后的价值。结果死亡组入院第1、3、7天外周血TIRAP、HBP水平及APACHEⅡ、SOFA评分高于生存组,FOXO3a水平低于生存组(P<0.05);入院第1天,脓毒症死亡患者TIRAP、HBP水平与APACHEⅡ、SOFA评分呈正相关,FOXO3a与APACHEⅡ、SOFA评分呈负相关(P<0.05);TIRAP×FOXO3a×HBP在脓毒症近期预后中存在交互作用(P<0.05);入院第1天外周血TIRAP+FOXO3a+HBP联合预测预后的曲线下面积(AUC)大于TIRAP+FOXO3a、TIRAP+HBP、FOXO3a+HBP,预测效能更佳(P<0.05)。结论脓毒症预后不良患者外周血TIRAP、HBP水平升高,FOXO3a水平降低,其水平变化与病情严重程度、近期预后有关,联合检测其水平可提高近期预后的预测效能。

Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants

Transcription factors (TFs) are key cellular components that control gene expression. They recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to specific regions of the genome where they can recruit transcriptional co-factors and/or chromatin regulators to fine-tune spatiotemporal gene regulation. Therefore, the identification of TFBSs in genomic sequences and their subsequent quantitative modeling is of crucial importance for understanding and predicting gene expression. Here, we review how TFBSs can be determined experimentally, how the TFBS models can be constructed in silico, and how they can be optimized by taking into account features such as position interdependence within TFBSs, DNA shape, and/or by introducing state-of-the-art computational algorithms such as deep learning methods. In addition, we discuss the integration of context variables into the TFBS modeling, including nucleosome positioning, chromatin states, methylation patterns, 3D genome architectures, and TF cooperative binding, in order to better predict TF binding under cellular contexts. Finally, we explore the possibilities of combining the optimized TFBS model with technological advances, such as targeted TFBS perturbation by CRISPR, to better understand gene regulation, evolution, and plant diversity.

Effects of calmodulin on DNA-binding activity of heat shock transcription factor in vitro

The DNA-binding activity of heat shocktranscription factor (HSF) was induced by heat shock (HS) of a whole cell extract. Addition of antiserum, specific toCaM, to a whole cell extract reduced bind of the HSF to the heat shock element (HSE) with maize, and the re-addition of CaM to the sample restored the activity of the HSF forbinding to HSE. In addition, DNA-binding activity of the HSF was also induced by directly adding CaM to a whole cell extract at non-HS temperature with maize. Similar resultswere obtained with wheat and tomato. Our observationprovide the first example of the involvement of CaM inregulation of the DNA-binding activity of the HSF.

Systematic identification and annotation of multiple-variant compound effects at transcription factor binding sites in human genome

Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential ＂interference＂ among multiple variants within the same TFBS. In this study, we presented COPE-TFBS （Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site）, a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression （GTEx） Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants.

A cost-effective ts CUT&Tag method for profiling transcription factor binding landscape

Knowledge of the transcription factor binding landscape(TFBL)is necessary to analyze gene regulatory networks for important agronomic traits.However,a low-cost and high-throughput in vivo chromatin profiling method is still lacking in plants.Here,we developed a transient and simplified cleavage under targets and tagmentation(tsCUT&Tag)that combines transient expression of transcription factor proteins in protoplasts with a simplified CUT&Tag without nucleus extraction.Our tsCUT&Tag method provided higher data quality and signal resolution with lower sequencing depth compared with traditional ChIP-seq.Furthermore,we developed a strategy combining tsCUT&Tag with machine learning,which has great potential for profiling the TFBL across plant development.

Structure-Based Prediction of Transcription Factor Binding Sites

Transcription Factors（TFs） are a very diverse family of DNA-binding proteins that play essential roles in the regulation of gene expression through binding to specific DNA sequences. They are considered as one of the prime drug targets since mutations and aberrant TF-DNA interactions are implicated in many diseases.Identification of TF-binding sites on a genomic scale represents a critical step in delineating transcription regulatory networks and remains a major goal in genomic annotations. Recent development of experimental high-throughput technologies has provided valuable information about TF-binding sites at genome scale under various physiological and developmental conditions. Computational approaches can provide a cost-effective alternative and complement the experimental methods by using the vast quantities of available sequence or structural information. In this review we focus on structure-based prediction of transcription factor binding sites. In addition to its potential in genomescale predictions, structure-based approaches can help us better understand the TF-DNA interaction mechanisms and the evolution of transcription factors and their target binding sites. The success of structure-based methods also bears a translational impact on targeted drug design in medicine and biotechnology.

TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites

Recent advances in the development of high-throughput tools have significantly revolutionized our understanding of molecular mech- anisms underlying normal and dysfunctional biological processes. Here we present a novel computational tool, transcription factor search and analysis tool （TrFAST）, which was developed for the in silico analysis of transcription factor binding sites （TFBSs） of sig- naling pathway-specific TFs. TrFAST facilitates searching as well as comparative analysis of regulatory motifs through an exact pattern matching algorithm followed by the graphical representation of matched binding sites in multiple sequences up to 50 kb in length. TrFAST is proficient in reducing the number of comparisons by the exact pattern matching strategy. In contrast to the pre-existing tools that find TFBS in a single sequence, TrFAST seeks out the desired pattern in multiple sequences simultaneously. It counts the GC con- tent within the given multiple sequence data set and assembles the combinational details of consensus sequence（s） located at these regions, thereby generating a visual display based on the abundance of unique pattern. Comparative regulatory region analysis of multi- ple orthologous sequences simultaneously enhances the features of TrFAST and provides a significant insight into study of conservation of non-coding cis-regulatory elements. TrFAST is freely available at http：//www.fi-pk.com/trfast.html.

Nucleosomal Context of Binding Sites Influences Transcription Factor Binding Affinity and Gene Regulation

Transcription factor （TF） binding to its DNA target site plays an essential role in gene regulation. The location, orientation and spacing of transcription factor binding sites （TFBSs） also affect regulatory function of the TF. However, how nucleosomal context of TFBSs influences TF binding and subsequent gene regulation remains to be elucidated. Using genome-wide nucleosome positioning and TF binding data in budding yeast, we found that binding affinities of TFs to DNA tend to decrease with increasing nucleosome occupancy of the associated binding sites. We further demonstrated that nucleosomal context of binding sites is correlated with gene regulation of the corresponding TF. Nucleosome-depleted TFBSs are linked to high gene activity and low expression noise, whereas nucleosome-covered TFBSs are associated with low gene activity and high expression noise. Moreover, nucleosome-covered TFBSs tend to disrupt coexpression of the corresponding TF target genes. We conclude that nucleosomal context of binding sites influences TF binding affinity, subsequently affecting the regulation of TFs on their target genes. This emphasizes the need to include nucleosomal context of TFBSs in modeling gene regulation.

Neuronal conversion from glia to replenish the lost neurons

Neuronal injury,aging,and cerebrovascular and neurodegenerative diseases such as cerebral infarction,Alzheimer’s disease,Parkinson’s disease,frontotemporal dementia,amyotrophic lateral sclerosis,and Huntington’s disease are characte rized by significant neuronal loss.Unfo rtunately,the neurons of most mammals including humans do not possess the ability to self-regenerate.Replenishment of lost neurons becomes an appealing therapeutic strategy to reve rse the disease phenotype.Transplantation of pluripotent neural stem cells can supplement the missing neurons in the brain,but it carries the risk of causing gene mutation,tumorigenesis,severe inflammation,and obstructive hydrocephalus induced by brain edema.Conversion of neural or non-neural lineage cells into functional neurons is a promising strategy for the diseases involving neuron loss,which may overcome the above-mentioned disadvantages of neural stem cell therapy.Thus far,many strategies to transfo rm astrocytes,fibroblasts,microglia,Muller glia,NG2 cells,and other glial cells to mature and functional neurons,or for the conversion between neuronal subtypes have been developed thro ugh the regulation of transcription factors,polypyrimidine tra ct binding protein 1(PTBP1),and small chemical molecules or are based on a combination of several factors and the location in the central nervous system.However,some recent papers did not obtain expected results,and discrepancies exist.Therefore,in this review,we discuss the history of neuronal transdifferentiation,summarize the strategies for neuronal replenishment and conversion from glia,especially astrocytes,and point out that biosafety,new strategies,and the accurate origin of the truly co nverted neurons in vivo should be focused upon in future studies.It also arises the attention of replenishing the lost neurons from glia by gene therapies such as up-regulation of some transc ription factors or downregulation of PTBP1 or drug interfe rence therapies.