• As a largest plant-specific transcription factor family, NAC domain proteins play an important role in plant development and regulation of abiotic stress tolerance. (frontiersin.org)
  • Assays showed that multiple proteins can bind to this sequence and that one of these is the transcription regulator delta-EF1 (dEF1). (usda.gov)
  • This promoter-enhancer also binds unidentified proteins that recognize a consensus estrogen response element (ERE) (Miller et al. (usda.gov)
  • Electromobility shift assays showed that the transcription regulator delta-EF1 (dEF1) is one of the proteins that recognize the E box region. (usda.gov)
  • The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. (elifesciences.org)
  • Acetylases are now known to modify a variety of proteins, including transcription factors, nuclear import factors and alpha-tubulin. (embl-heidelberg.de)
  • Transcription is regulated through the binding of transcription factor proteins to specific cis -level regulatory sites in the DNA. (ucsc.edu)
  • For example, some proteins activate transcription by recruiting RNA polymerase, some repress transcription by suppressing this recruitment, and others insulate proximal regions from the activity of nearby transcriptional activators or repressors. (ucsc.edu)
  • ChIP utilizes antibodies that selectively recognize and bind proteins, including histones, histone modifications, transcription factors, and cofactors, to provide information about chromatin states and gene transcription. (cellsignal.com)
  • Once the chromatin immunoprecipitation itself is complete, several downstream analyses can be conducted on the purified chromatin and the associated proteins, histones, transcription factors, and cofactors. (cellsignal.com)
  • They attract transcription factor proteins that start the expression of genes, thereby "enhancing" their activity. (mpg.de)
  • According to the prevailing theory, transcription factor proteins recognize "codewords" in enhancers that are specific for a certain cell type, allowing the genome to tell a cell's story by jumping to the right chapters. (mpg.de)
  • Transcription factors help to regulate gene expression-turning genes on or off and dialing up or down their level of activity-often in partnership with the proteins that they bind. (mit.edu)
  • Transcription factors are a well-known family of proteins, but new research from Whitehead Institute Member Richard Young and colleagues shows that the picture we have had of them is incomplete. (mit.edu)
  • Gene activation is dependent on cell-specific transcription factors that recognize transcriptional enhancer sequences. (imperial.ac.uk)
  • A long virus promoter construct that included sequences downstream from the transcription start point (TSP) expressed lower levels of EGFP than a shorter sequence that stopped at the TSP. (usda.gov)
  • Diverse KRAB-ZFPs recognize specific DNA sequences with the majority targeting endogenous retroviruses, ensuring their repression. (elifesciences.org)
  • It is proposed that this relaxed property of finger 1 allows transcription factor Sp1 to bind various DNA sequences with high affinity. (rcsb.org)
  • This generally yields a large library of DNA sequences, including some that were bound by the transcription factor directly, some that were bound indirectly via interactions with other molecules, and some false positives (such as cases of nonspecific binding). (ucsc.edu)
  • Consistent with earlier observations based on partial sequences of ORF11 and ORF056, F14.1158H grouped clearly closer to PPVs than other poxviruses (Figure, panel A), although distinctly separate from the 5 recognized species (Figure, panels B-D). We found the amino acid sequences to be more similar to PPV species than to other chordopoxviruses. (cdc.gov)
  • With a series of statistical and bioinformatic analyses, the scientists identified several hundreds of tissue-specific DNA subsequences or "codewords" in enhancers that guide transcription factors, not only confirming sequences already known from other studies, but also identifying many new ones. (mpg.de)
  • The researchers developed a program that is able to identify DNA sequences that are recognized by the cell in order to activate genes in a tissue-specific way. (mpg.de)
  • the majority of human transcription factors contain an ARM-like region between their DNA and protein binding regions, and these sequences were conserved across animal species. (mit.edu)
  • 2 − 6 These nuclease-resistant polymers persist in live organisms for days and are typically designed to recognize 25-base sequences that span intron-exon junctions or translational start sites. (cdc.gov)
  • This protein represents a large fungal family of transcription factors, Gal4 family, which includes over 50 members in the yeast Saccharomyces cerevisiae e.g. (wikipedia.org)
  • Two executive domains, DNA binding and activation domains, provide key function of the Gal4 protein conforming to most of the transcription factors. (wikipedia.org)
  • As a part of the Gal4 regulation, inhibitory protein Gal80 recognises and binds to the Gal4 region (853-874 aa). (wikipedia.org)
  • The Gal4 protein interacts also with other mediators of transcription as are Tra1, TAF9, and SAGA/MED15 complex. (wikipedia.org)
  • The encoded protein recognizes an Ephrussi-box ('E-box') binding site ('CANNTG') - a motif first identified in immunoglobulin enhancers. (nih.gov)
  • Using semi-quantitative reverse-transcription polymerase chain reaction (RT-PCR) and western blots experiments, we compared changes in ETS-1 and ETS-2 expression, their protein levels, and the regulation of some of their target gene expressions at different stages of the ocular tumoral progression in the transgenic mouse model, Tyrp-1-TAg, with those in normal eyes from control mice of the same age. (molvis.org)
  • In addition, Kayed et al ( 15 ) demonstrated that RUNX2 was overexpressed in PC and could be regulated by certain cytokines, including transforming growth factor β1 and bone morphogenetic protein 2. (spandidos-publications.com)
  • A key characteristic of each transcription factor protein is its DNA binding domain. (ucsc.edu)
  • The principle behind ChIP is relatively straightforward and relies on the use of an antibody to isolate, or precipitate, a certain protein, histone, transcription factor, or cofactor and its bound chromatin from a protein mixture that was extracted from cells or tissues. (cellsignal.com)
  • Here, we tested the hypothesis that the DNA repair protein OGG1 recognizes 8-oxoguanine (8-oxoGua) in promoters modulating IFN expression. (lu.se)
  • Although the TATA-Binding Protein (TBP) subunit of TFIID is necessary and sufficient for in vitro transcription, the TBP-Associated Factor (TAF) subunits recognize downstream promoter elements, act as co-activators, and interact with nucleosomes. (biorxiv.org)
  • In a paper published in Molecular Cell on July 3 , Young and postdocs Ozgur Oksuz and Jonathan Henninger reveal that along with DNA and protein, many transcription factors can also bind RNA. (mit.edu)
  • Young, Oksuz and Henninger got their biggest clue that researchers might be overlooking something from the human immunodeficiency virus (HIV), which produces a transcription factor-like protein called Tat. (mit.edu)
  • rsos from in silico dynamical modelling by tuning parameters for protein concentrations and other factors .r o y involved in the rate equations describing the systems. (lu.se)
  • Computational analysis of microbial genomes has suggested that many factors function optimally when in a particular orientation and position with respect to their target promoters. (nih.gov)
  • We found evidence of non-random organization of sites within promoters, differences in binding site density, or both for thirty-eight transcription factors. (nih.gov)
  • We propose a new model in which TAFs function as reinitiation factors, accounting for the differential responses of promoters to various transcription factor mutations. (biorxiv.org)
  • Activates transcription from class II MHC promoters. (lu.se)
  • It forms a Zn - cysteines thiolate cluster, and specifically recognizes UASG in GAL1 promoter. (wikipedia.org)
  • Cotransfection assays were done, using expression vectors for thyroid receptor (TR) or chicken ovalbumin upstream promoter transcription factor 1 (COUP-TF1) to increase the levels of these hormone receptors in the cells containing the CAV promoter driving expression of EGFP. (usda.gov)
  • Cotransfection assays, using expression vectors for thyroid receptor (TR) or chicken ovalbumin upstream promoter transcription factor 1 (COUP-TF1) and the CAV promoter driving expression of EGFP, were used to test for transcription regulation by these members of the nuclear receptor family that also recognize a consensus ERE. (usda.gov)
  • Within this core promoter region we recognized functional binding sites for TFAP2 transcription factors and identified TFAP2 as repressors of the TBX20 gene in vitro and in vivo. (nih.gov)
  • We show that these signatures allow transcription factors with substantial differences in binding site specificity to share similar promoter specificities. (nih.gov)
  • TFIID binds promoter DNA to recruit RNA polymerase II and other basal factors for transcription. (biorxiv.org)
  • Here we show that transcription induces stable TAF binding to downstream promoter DNA, independent of upstream contacts, TBP, or other basal transcription factors. (biorxiv.org)
  • This transcription-dependent TAF complex promotes subsequent activator-independent transcription, and promoter response to TAF mutations in vivo correlates with the level of downstream, rather than overall, Taf1 crosslinking. (biorxiv.org)
  • The NAC domain transcription factors in Arabidopsis function in plant development, senescence, and stress regulation. (frontiersin.org)
  • Additionally, the regulation of the DNA binding of the transcriptional activators after stimulation is quantified using chromatin immunoprecipitation, employing epitope-tagged factors and real-time qPCR. (srce.hr)
  • This tested for transcription regulation by these members of the nuclear receptor family that also recognize a consensus ERE. (usda.gov)
  • Thus, the bromodomain is functionally linked to the HAT activity of co-activators in the regulation of gene transcription. (embl-heidelberg.de)
  • Many processes in parasite biology involve changes at the chromatin level, including regulation of transcription along a complex life cycle, delimitation of functional elements in the genome, and antigenic variation. (plos.org)
  • The nature of this regulation depends on the transcription factor. (ucsc.edu)
  • With the appropriate analysis methods, ChIP-seq can be a valuable approach for elucidating transcription factor binding and cis -level regulation. (ucsc.edu)
  • The short length and high degeneracy of sites recognized by DNA-binding transcription factors limit the amount of information they can carry, and individual sites are rarely sufficient to mediate the regulation of specific targets. (nih.gov)
  • This rethinking of how transcription factors work may lead to a better understanding of gene regulation, and may provide new targets for RNA-based therapeutics. (mit.edu)
  • In some processes, chromatin modifications carry heritable regulatory information that is transmitted from mother to daughter cells, whereas in other cases, they are implicated in the execution of the information contained in the DNA sequence, or occur as a consequence of dynamic nuclear processes such as transcription. (plos.org)
  • Pickett's team reported that ARE is one of the motifs required for xenobiotics-induced activation of transcription of the GST Ya gene and also defined the ARE consensus sequence . (asbmb.org)
  • By comparing sequence data between the tissues, the program learned to recognize sequence patterns in enhancers that are characteristic for certain tissues. (mpg.de)
  • Aim: To understand how transcriptional factors Pdr1 and Pdr3, belonging to the pleiotropic drug resistance system, are activated, and regulated after introducing chemical toxins to the cell in the model organism Saccharomyces cerevisiae. (srce.hr)
  • Results: Our results indicated higher expression levels of the Pdr1 transcriptional factor, compared to its homologous Pdr3 after treatment with menadione. (srce.hr)
  • The results indicate that Pdr1 is most abundant after 30 minutes from the beginning of the treatment, compared with 240 minutes after the treatment when the function of the transcription factor is faded. (srce.hr)
  • One possibility is that Pdr1, after recognizing the xenobiotic menadione, is removed by a degradation mechanism. (srce.hr)
  • It is possible that overexpressing the part of Pdr1 which recognizes menadione alone was sufficient to detoxify and hence produce a tolerance towards menadione. (srce.hr)
  • DNA polymerase (ORF025), early transcription factor (ORF083), DNA-directed RNA polymerase subunit RPO132 (ORF101), and DNA topoisomerase type 1 (ORF062) ( Figure ). (cdc.gov)
  • This kit recognizes Rat RUNX2 in samples. (caslab.com)
  • Using bioinformatics, a luciferase reporter assay and western blot analyses, the current study identified that runt‑related transcription factor 2 (RUNX2) was a target of miR‑205 in PC and overexpression of miR‑205 suppressed the expression of RUNX2. (spandidos-publications.com)
  • Runt-related transcription factor 2 (RUNX2), a member of the RUNX family, functions as a critical regulator for osteoblast differentiation ( 14 ). (spandidos-publications.com)
  • Here we present analysis of transcription factor binding motifs co-localized with non-coding variants. (biomedcentral.com)
  • Further analysis of transcription factors with conserved binding motifs can reveal cell regulatory pathways crucial for the survivability of various human cancers. (biomedcentral.com)
  • To understand the DNA recognition mechanism of zinc finger motifs of transcription factor Sp1, we have determined the solution structure of DNA-binding domain of the Sp1 by solution NMR techniques. (rcsb.org)
  • These motifs tend to be short and degenerate, so even when the DNA binding motif is known, one cannot generally predict where a given transcription factor may bind. (ucsc.edu)
  • The type I IFN signaling pathway includes toll-like receptor 3 ( TLR3 ) and interferon regulator factor 7 ( IRF7 ). (cdc.gov)
  • We establish that IGF-II-induced HIF2A/EPAS1 expression during hypoxia is due to de novo transcription and further present the estrogen-related receptor alpha (ERRα) transcription factor as a positive regulator of HIF2A. (lu.se)
  • There is even a conserved structure, the bromodomain, that recognizes acetylated residues and may serve as a signalling domain. (embl-heidelberg.de)
  • From DNA-binding analysis performed by NMR and comparison between structures determined here and previously reported structures of other zinc fingers, it was assumed that DNA recognition modes of fingers 2 and 3 would be similar to those of fingers of Zif268, in which each finger recognizes four base pairs strictly by using residues at positions -1, 2, 3, and 6 of the recognition helix. (rcsb.org)
  • No. 562247), fixed and permeabilized using the BD Pharmingen™ Transcription Factor Buffer Set (Cat. (bdbiosciences.com)
  • Applications Tested: This Dan11mag antibody has been tested by intracellular flow cytometric analysis of mouse splenocytes using the Foxp3/Transcription Factor Staining Buffer Set (cat. (thermofisher.com)
  • Description: This Dan11mag antibody recognizes Eomesodermin (Eomes), also known as T-box brain 2 (TBR2). (thermofisher.com)
  • A number of factors have recently contrib- a specific immune response, mediated by multiple mechanisms, uted to an increase in the attention focused on hypersensitivity including IgE antibody. (cdc.gov)
  • This enhancement is combined with the activation of Pdx-1, the transcription factor that regulates insulin gene expression. (lu.se)
  • It also modulates gene transcription and recombination [ 7 ]. (hindawi.com)
  • These data reveal a novel mechanism by which a transcription factor localizes to motile cilia and modulates cell activities including cilia motility and inflammation response. (cdc.gov)
  • Each DNA binding domain recognizes and interacts with DNA that matches a specific nucleotide pattern, or motif. (ucsc.edu)
  • Galactose induces Gal4 mediated transcription albeit Glucose causes severe repression. (wikipedia.org)
  • This gene encodes transcription factor 4, a basic helix-loop-helix transcription factor. (nih.gov)
  • HER2/neu (also called ERB B2 ) is the gene that encodes the human epidermal growth factor receptor type 2. (cancerquest.org)
  • Here, we confirmed that SISTER OF TM3 (STM3), a homolog of Arabidopsis SOC1, is a major positive regulatory factor of tomato inflorescence architecture by map-based cloning. (nature.com)
  • TLR3 acts earlier in the pathway and recognizes double stranded viral RNA, while IRF7 is a transcription factor to initiate IFN production. (cdc.gov)
  • Initially, researchers were mainly focused on miRNA identification, appropriate to specific or multiple environmental condition, expression profiling and recognize their roles in stress tolerance. (intechopen.com)
  • Transactivation assay in yeast cells revealed that CmNAC1 functions as a transcription activator, and its transactivation domain is located in the C-terminus. (frontiersin.org)
  • Here we report the solution structure of the bromodomain of the HAT co-activator P/CAF (p300/CBP-associated factor). (embl-heidelberg.de)
  • The role of two members of the ETS (E26 avian leukemia oncogene) family of transcription factors, ETS-1 and ETS-2, has been investigated in many cancers but has not yet been studied in ocular tumors. (molvis.org)
  • The T-box family of transcription factors has been shown to have major impact on human development and disease. (nih.gov)
  • Although many people with schizophrenia do not have a family history, genetic factors are strongly implicated. (msdmanuals.com)
  • These findings suggest that the ROS-generated epigenetic mark 8-oxoGua via its reader OGG1 serves as a homeostatic thresholding factor in IFN-λ expression. (lu.se)
  • 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)
  • We illustrate how spatial information dictating the positioning and density of binding sites can in principle increase the information available to the organism for differentiating a transcription factor's true targets, and we indicate how this information could potentially be leveraged for the same purpose in bioinformatic analyses. (nih.gov)
  • Generally, stress induce miRNAs-based inhibition of their target mRNAs, however, positive transcription factors accumulated and become more active after mRNA inhibition. (intechopen.com)
  • Proteolytic turnover of the Gal4 transcription factor is not required for function in vivo. (wikipedia.org)
  • Next, the researchers tested to see if RNA binding affected the transcription factors' function. (mit.edu)
  • For example, we have applied light-activatable cMOs to interrogate transcription factor function during zebrafish notochord, pancreas, and vascular patterning. (cdc.gov)
  • Aging is a recognized risk factor for T2D development, and the decline in pancreatic β-cell function is linked to genetic changes during aging. (lu.se)
  • Our results indicated that CmNAC1 is a critical factor in ABA signaling pathways and it can be utilized in transgenic breeding to improve the abiotic stress tolerance of crops. (frontiersin.org)
  • In summary, we have identified, and at the molecular level characterized, signaling pathways and specific factors through which oncogenic HIF2A activity is regulated and may be targeted. (lu.se)
  • Using a mouse model of organic dust-induced airway inflammation, we found that the transcription factor serum response factor (SRF) localizes to motile cilia of airway epithelial cells and alters its localization in response to inflammatory stimuli. (cdc.gov)
  • TCF4 is a widely used alternative name for T-cell-specific transcription factor 4 (TCF7L2) conflicting with the official symbol for transcription factor 4 (TCF4). (nih.gov)
  • Motile cilia harbor serum response factor as a mechanism of environment sensing and injury response in the airway. (cdc.gov)
  • However, no transcription factors are known to be regulated by cilia localization as a sensing mechanism in vertebrates. (cdc.gov)
  • Most human diseases are caused by the interplay between numerous genetic and environmental factors, and infectious diseases are no exception. (cdc.gov)
  • The researchers wondered if Tat might be more similar to human transcription factors than anyone had realized. (mit.edu)
  • One of these transcriptional regulators is nuclear factor erythroid 2-related factor 2, or NRF2, identified in 1994 by another research group. (asbmb.org)
  • OBJECTIVE- Chronic activation of the nuclear factor-κB (NF-κB) in white adipose tissue leads to increased production of pro-inflammatory cytokines, which are involved in the development of insulin resistance. (diabetesjournals.org)
  • The reason that researchers had not recognized transcription factors' RNA binding region as such is because it is not a typical RNA binding domain. (mit.edu)
  • As shown below, binding of the growth factor can lead to cell division. (cancerquest.org)
  • The aryl hydrocarbon receptor (AhR) transcription factor is increasingly recognized as functioning in cell cycle control. (aspetjournals.org)
  • Large cell neuroendocrine carcinoma (LCNEC) is now recognized as a histologically high grade non small cell carcinoma showing histopathological features of neuroendocrine differentiation as well as immunohistochemical neuroendocrine markers. (ersjournals.com)
  • We explore the method on three circuits for haematopoiesis and embryonic stem cell development for commitment and reprogramming scenarios and illustrate how the method can be used to determine sequential steps for onsets of external factors, essential for efficient reprogramming. (lu.se)