• Finally, we constructed the drug, transcription factors (TFs), and microRNA network of the diagnostic genes. (nature.com)
  • A regulatory factor X transcription factor that is required for the expression of MHC CLASS II GENES . (online-medical-dictionary.org)
  • Furthermore, to confirm whether the regulatory role of RUNX2 in the expression of these genes is related to its binding to the promoter region, we performed chromatin immunoprecipitation (ChIP) assays. (unab.cl)
  • Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in regulatory networks or cascades. (wikipedia.org)
  • A typical gene regulatory network looks something like this: The nodes of this network can represent genes, proteins, mRNAs, protein/protein complexes or cellular processes. (wikipedia.org)
  • Furthermore, putative ATF3 regulatory elements were identified within the promoters of ATF3 target genes and were confirmed by ChIP-Seq. (oncotarget.com)
  • Significantly differentially expressed (SDE) immunological genes and transcription factor (TF) were selected for functional pathways and transcriptional signaling identification. (frontiersin.org)
  • Twenty-four potential transcriptional regulatory pathways were identified based on SDE TFs matched with their corresponding SDE immunological genes. (frontiersin.org)
  • The physiological conditions experienced by a microbial community can thus be inferred using meta-transcriptomic sequencing by comparing transcription levels of specifically chosen genes. (osti.gov)
  • Sample-specific meta-genomic assembled genomes (MAGs) were used as reference genomes to accurately identify the origin of RNA reads, and transcript ratios of genes with opposite transcription responses were compared to eliminate biases related to differences in organismal abundance, an approach hereafter named the "diametric ratio" method. (osti.gov)
  • This gene encodes a transcription factor that regulates MHC class II genes by binding to a promoter element referred to as an X box. (cancerindex.org)
  • The isoform encoded by the unspliced mRNA, XBP1(U), is constitutively expressed, and thought to function as a negative feedback regulator of XBP1(S), which shuts off transcription of target genes during the recovery phase of ER stress. (cancerindex.org)
  • INTRODUCTION broken, which in realistic situations can severly constrain the Transcriptional regulation of effector genes is a highly successful regulatory options. (lu.se)
  • Sterol regulatory element-binding proteins (SREBPs) compose a family of transcriptional factors that regulate the expression of various genes required for the synthesis of phospholipids, fatty acids, and cholesterol. (novusbio.com)
  • Transcription factors are proteins that regulate the transcription of genes, or the production of mRNA from DNA. (biolegend.com)
  • The underphosphorylated, active form of Rb interacts directly with E2F1 , leading to cell cycle arrest, while the hyperphosphorylated form decouples from E2F1, thus promoting the transcription of genes promoting entry into the S phase. (biolegend.com)
  • In particular, mutations in DNA binding sites recognized by transcription factors can alter regulator binding affinities and, consequently, expression of target genes. (biomedcentral.com)
  • Exons 1-6 of the WT1 gene encode the regulatory domain, which regulates expression of target genes, and exons 7-10 encode the 4 zinc fingers of the DNA-binding region of the WT1 protein. (medscape.com)
  • The WT1 protein mediates the mesenchymal-epithelial transition and differentiation during morphogenesis of the kidney and gonad by repressing genes that encode cell proliferation factors and by activating genes that encode markers of epithelial cell differentiation. (medscape.com)
  • The regulator can be DNA, RNA, protein or any combination of two or more of these three that form a complex, such as a specific sequence of DNA and a transcription factor to activate that sequence. (wikipedia.org)
  • Characterization of SAP-1, a protein recruited by serum response factor to the c-fos serum response element. (nih.gov)
  • GS-002 also induced endoplasmic reticular (ER) stress as evidenced by increases in ER stress-responsive proteins including glucose-regulated protein 78 (GRP78), growth arrest- and DNA damage-inducible gene 153 (GADD153), phosphorylated eukaryotic initiation factor 2 α (eIF2 α ), phosphorylated protein endoplasmic-reticular-resident kinase (PERK), and ATF-3. (hindawi.com)
  • I will start my discussion by introducing the importance of studies of protein interactions for understanding of biological regulatory specificity. (hstalks.com)
  • By controlling the level of transcription, this process can determine when and how much protein product is made by a gene. (medlineplus.gov)
  • This gene product is a bZIP protein, which was also identified as a cellular transcription factor that binds to an enhancer in the promoter of the T cell leukemia virus type 1 promoter. (cancerindex.org)
  • Here, we demonstrate that the endoplasmic reticulum stress sensor inositol-requiring enzyme 1 (IRE1α) and its substrate transcription factor X-box-binding protein 1 (XBP1) drive NK cell responses against viral infection and tumors in vivo. (cancerindex.org)
  • Transcription regulatory protein SNF2 (EC 3.6.4. (weizmann.ac.il)
  • RANK binds to transmembrane protein nuclear factor-κB receptor activating factor ligand (RANKL) to activate RANK/RANKL, TRAF6/RANKL/MAPKs, TRAF6/ RANKL/NF-κB, Wnt/RANKL/RANKL, and JAK2/STAT3/RANKL. (frontiersin.org)
  • The encoded protein contains two different binding sites that are known to bind DNA and function as a regulator of gene transcription. (biolegend.com)
  • STAT3 protein belongs to a group of intracellular transcription factors that mediate a variety of functions such as cellular differentiation, proliferation, and apoptosis. (biolegend.com)
  • The WT1 protein is a transcription factor predominantly expressed in the embryonic kidneys and gonads. (medscape.com)
  • The tat protein stimulates LONG TERMINAL REPEAT-driven RNA synthesis for both viral regulatory and viral structural proteins. (bvsalud.org)
  • RFXANKbase: Mutation registry for Ankyrin repeat containing regulatory factor X-associated protein deficiency. (lu.se)
  • The TAL1/SCL transcription factor regulates cell cycle progression and proliferation in differentiating murine bone marrow monocyte precursors. (nih.gov)
  • RUNX1 belongs to the runt domain family of transcription factors and regulates target gene expression through forming a heterodimeric DNA-binding complex with CBFB. (biolegend.com)
  • RUNX1 regulates CD4 gene transcription during multiple stages of T cell development and represses the CD4 gene in CD4-CD8- (double negative) T cells. (biolegend.com)
  • A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell. (wikipedia.org)
  • At one level, biological cells can be thought of as "partially mixed bags" of biological chemicals - in the discussion of gene regulatory networks, these chemicals are mostly the messenger RNAs (mRNAs) and proteins that arise from gene expression. (wikipedia.org)
  • Proteins of the TCF subfamily form a ternary complex by binding to the the serum response factor and the serum reponse element in the promoter of the c-fos proto-oncogene. (nih.gov)
  • Signals from the environment or from other cells activate proteins called transcription factors. (medlineplus.gov)
  • These proteins bind to regulatory regions of a gene and increase or decrease the level of transcription. (medlineplus.gov)
  • Once the transcription factor binds to an enhancer region, this can cause stimulation or repression of gene transcription. (biolegend.com)
  • Orthologous to human TAL1 (TAL bHLH transcription factor 1, erythroid differentiation factor). (nih.gov)
  • Genome-Wide Identification of bHLH Transcription Factor in Medicago sativa in Response to Cold Stress. (bvsalud.org)
  • In higher plants , the bHLH transcription factors play pleiotropic regulatory roles in response to abiotic stresses . (bvsalud.org)
  • The Regulatory Genome. (nature.com)
  • The fully sequenced genome, since compact and unduplicated, gives acces to regulatory DNA segments, isolated for reporter gene essays in vivo . (uibk.ac.at)
  • Recent studies revealed pervasive binding of p53 to cis-regulatory elements (CREs), which are non-coding segments of DNA that spatially and temporally control transcription through the combinatorial binding of local transcription factors. (whiterose.ac.uk)
  • We focus on novel combinatorial codes for transcription factors as nuclear effectors of major signaling pathways, including Wnt and FGF/MEK signaling. (uibk.ac.at)
  • Several transcription factors important in embryonic development are abnormally expressed in adult tissues and thus participate in the activation of signaling pathways related to the acquisition of the tumor phenotype. (unab.cl)
  • Further analysis of transcription factors with conserved binding motifs can reveal cell regulatory pathways crucial for the survivability of various human cancers. (biomedcentral.com)
  • Predicted to be part of transcription regulator complex. (nih.gov)
  • Koide, T., Hayata, T. & Cho, K. W. Y. Xenopus as a model system to study transcriptional regulatory networks. (nature.com)
  • Pax6 is a transcription factor present during embryonic development. (biolegend.com)
  • Its differentiation and function are mainly regulated by macrophage colony-stimulating factor (M- CSF), receptor activator of nuclear factor kappa B(RANK) ( 7 ). (frontiersin.org)
  • This development occurs under the influence of macrophage colony-stimulating factor (M-CSF), which is secreted by various cell types (eg, endothelial cells, fibroblasts). (msdmanuals.com)
  • The master tumor suppressor p53 controls transcription of a wide-ranging gene network involved in apoptosis, cell cycle arrest, DNA damage repair, and senescence. (whiterose.ac.uk)
  • Thus, the present study is aimed at evaluating the role of the RUNX2 transcription factor in inhibiting the apoptosis process. (unab.cl)
  • Activating transcription factor-(ATF-) 3, a stress-inducible transcription factor, is rapidly upregulated under various stress conditions and plays an important role in inducing cancer cell apoptosis. (hindawi.com)
  • Differential IkappaB kinase activation and IkappaBalpha degradation by interleukin-1beta and tumor necrosis factor-alpha in human U937 monocytic cells. (nih.gov)
  • See Wilms Tumor: A Pediatric Oncology Success Story , a Critical Images slideshow, to help identify the clinical features, staging evaluation, prognostic factors, and therapeutic options for this disease. (medscape.com)
  • All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. (osti.gov)
  • and regulation of transcription by RNA polymerase II. (nih.gov)
  • Identification of ETS-like transcription factor 4 as a novel androgen receptor target in prostate cancer cells. (nih.gov)
  • Gene expression profiling of ErbB receptor and ligand-dependent transcription. (rochester.edu)
  • We designed and executed a massively parallel reporter assay (MPRA) to investigate the effect of transcription factor binding motifs and local sequence context on p53-bound CRE activity. (whiterose.ac.uk)
  • Our data indicate that p53-bound CREs are both positively and negatively affected by alterations in local sequence context and changes to co-regulatory TF motifs. (whiterose.ac.uk)
  • Here we present analysis of transcription factor binding motifs co-localized with non-coding variants. (biomedcentral.com)
  • Gene regulatory networks (GRNs) provide system level explanations of developmental and physiological functions in the terms of the genomic regulatory code. (nature.com)
  • Stathopoulos, A. & Levine, M. Genomic regulatory networks and animal development. (nature.com)
  • For example, the UK Biobank , a leading cohort study of half a million persons, has collected genomic, clinical and risk factor information and has contributed to numerous discoveries in human genetics. (cdc.gov)
  • Master regulatory GATA transcription factors: mechanistic principles and emerging links to hematologic malignancies. (rochester.edu)
  • Satou, Y. (2020): Gata is ubiquitously required for the earliest zygotic gene transcription in the ascidian embryo. (uibk.ac.at)
  • Although the role of p53 as a strong trans-activator of gene expression is well known, the co-regulatory factors and local sequences acting at p53-bound CREs are comparatively understudied. (whiterose.ac.uk)
  • Similar to SREBP-1a and SREBP-1c, SREBP-2 acts by first binding to sterol regulatory DNA sequences, and subsequently up-regulating the synthesis of enzymes involved in sterol biosynthesis. (novusbio.com)
  • RUNX2 is the transcription factor responsible for osteogenic differentiation in mammals. (unab.cl)
  • OB mediates bone formation through runt-related transcription factor 2(Runx2). (frontiersin.org)
  • Runx2 is a critical regulatory factor promoting OB maturation in early differentiation. (frontiersin.org)
  • The capability of these cells to differentiate depends on the stem cell type, the regulation of gene expression by various transcription factors and interaction with the stem cell niche 1,4 . (biolegend.com)
  • The Role of MB0, MBI and MBII in Interaction and Dynamics of the Master Regulatory Transcription Factor c-Myc. (lu.se)
  • Located within the intrinsically disordered N-terminus part of c-Myc are the highly conserved so-called Myc boxes (MB0-IV), which are crucial for Myc function and interaction with other transcription factors. (lu.se)
  • The resulting loss of 26 nt from the spliced mRNA causes a frame-shift and an isoform XBP1(S), which is the functionally active transcription factor. (cancerindex.org)
  • We also found an unexpectedly dynamic pattern of transcript isoform regulation, suggesting a critical regulatory role during HSC differentiation, and a cell cycle/DNA repair signature associated with multipotency in MPP2 cells. (lu.se)
  • However, this perennial plant is native to warmer temperate regions, and its valuable cold - acclimation -related regulatory mechanisms are still less known. (bvsalud.org)
  • This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. (osti.gov)
  • However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. (osti.gov)
  • In this paper, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "σ-finger" of the bacterial transcription initiation factor σ. (osti.gov)
  • and regulation of transcription, DNA-templated. (nih.gov)
  • Gene regulation can occur at any point during gene expression, but most commonly occurs at the level of transcription (when the information in a gene's DNA is passed to mRNA). (medlineplus.gov)
  • Optimizing the parameters of the regulatory system allows us to quantify the fitness benefit of regulation. (lu.se)
  • In unicellular organisms like E. coli and yeast, the benefits of between potential cost and benefit, regulation can make the most a well-adapted regulatory system are readily quantified, as the difference to the long-term growth rate if the resource in question fitness of an individual can be estimated by its growth rate in is only available a similarly small fraction of the time. (lu.se)
  • Over evolutionary time scales, regulation must provide a fitness benefit that offsets the costs of maintaining the regulatory system. (lu.se)
  • The expression of the transcription factor ATF3 was elevated in human CRC specimens in a TMA by immunochemistry analysis compared to the adjacent normal tissues. (oncotarget.com)
  • Our data reveal the differential expression landscape of 493 transcription factors and 682 lncRNAs and highlight specific expression clusters operating in HSCs. (lu.se)
  • The expression and transcription of alkaline phosphatase (ALP) and BSP promote the maturation and mineralization of OB ( 5 ). (frontiersin.org)
  • Alterations in expression of confirmed miR-210 transcription factor target foxp3 were observed in the dLN and ears and decreases in predicted targets' (foxp3, runx1, runx3, and smad4) mRNA expression were observed in the dLN of TDI-exposed mice. (cdc.gov)
  • Interestingly, the phylogenetic analysis and conserved motif screening of the cold -induced MsbHLHs showed that the expression pattern is relatively varied in each bHLH subfamily, this result indicating that the 65 MsbHLHs may be involved in a complex cold -responsive regulatory network. (bvsalud.org)
  • Less understood is the mechanism of epigenetics by which chromatin modification may provide cellular memory by blocking or allowing transcription. (wikipedia.org)
  • We explore diverse elements associated with the evolution of regulatory networks, such as gene duplication, where new interactions can emerge together with their upstream and downstream binding sites. (caister.com)
  • EVI1 Interferes with Myeloid Maturation via Transcriptional Repression of Cebpa, via Binding to Two Far Downstream Regulatory Elements. (rochester.edu)
  • REforge Associates Transcription Factor Binding Site Divergence in Regulatory Elements with Phenotypic Differences between Species. (mpg.de)
  • The structures reveal that-for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "σ-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ~5 nt to ~10 nt. (osti.gov)
  • Based on previous studies, this review will summarize the regulatory network mechanism of ferroptosis on bone remodeling and reveal the role of ferroptosis in osteoporosis (OP). (frontiersin.org)
  • Forkhead box (Fox) transcription factors evolved early in animal evolution and represent important components of conserved gene regulatory networks (GRNs) during animal development. (lu.se)
  • Our data demonstrate negative selection against binding sites alterations and suggest that such selection pressure protects cancer cells from rewiring of regulatory circuits. (biomedcentral.com)
  • e.g. inflammation, genotoxicity, and This chapter focuses on issues as- ellers, growth factors, growth factor epigenetic alterations) and can have sociated with the understanding and receptors, signal transducers, and both genetic and epigenetic origins. (who.int)
  • 1) the mechanisms and dynamics for gene regulatory switches affecting the pluripotent ectoderm in vivo . (uibk.ac.at)
  • Dysfunction of the regulatory mechanisms maintaining this balance between active immunity and tolerance in the gut may lead to mucosal inflammation and damage and GI diseases. (medscape.com)
  • In this study, the role of the transcriptional activator IFN regulatory factor-1 (IRF-1) in murine NK cell activity was assessed. (silverchair.com)
  • Transcription factors have an important role in the ability of a cell to self-renew and also differentiate into most cell types, also known as pluripotency 1 . (biolegend.com)
  • Implementing large scale studies across different populations could substantially enhance efforts to uncover the role of genetic factors in various diseases. (cdc.gov)
  • Developmental gene regulatory networks in the zebrafish embryo. (nature.com)
  • In addition, ATF3 overexpression associated with a regulatory molecular signature, and its functions are related to the pathogenic development of CRC. (oncotarget.com)
  • These molecules and their interactions comprise a gene regulatory network. (wikipedia.org)
  • In my presentation I will discuss transcription factor interactions. (hstalks.com)
  • Efficient functional readout, notably at DNA level in vivo is often complicated by the complexity of regulatory interactions and the complexity of genomes, particularly in vertebrates. (uibk.ac.at)
  • We will present first molecular data showing how these boxes interact with critical transcription factors as well as with each other in a highly specific but also highly dynamic manner, and how these interactions can be interrupted. (lu.se)
  • Peter, I. S. & Davidson, E. H. The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage. (nature.com)
  • Such DNA constructs, when electroporated in fertilised eggs, produce transiently transgenic embryos and allow rapid gene functional and gene regulatory analyses , in precisely identifyable tissue precursors, from earliest embryonic stages in vivo . (uibk.ac.at)
  • The major risk factors include chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, environmental carcinogens such as aflatoxin B1 (AFB1), alcoholic cirrhosis, and inherited genetic disorder such as hemochromatosis, Wilson's disease, and tyrosinemia. (hindawi.com)
  • New studies will need to focus on enhancers and transcription factors, as well as genetic regulatory networks, and how changes in these networks can impact health and disease. (cdc.gov)