AnatomyOrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsInformation Science
Genes, HomeoboxHomeodomain ProteinsTranscription FactorsTranscription, GeneticDNA-Binding ProteinsPromoter Regions, GeneticMolecular Sequence DataBase SequenceGene Expression RegulationSp1 Transcription FactorBinding SitesTrans-ActivatorsTranscriptional ActivationGene Expression Regulation, DevelopmentalRepressor ProteinsNuclear ProteinsProtein BindingAmino Acid SequenceBasic Helix-Loop-Helix Transcription FactorsRNA, MessengerDNAAntennapedia Homeodomain ProteinCell LineTranscription Factor AP-1Paired Box Transcription FactorsMutationForkhead Transcription FactorsSignal TransductionCell DifferentiationCell NucleusTransfectionBasic-Leucine Zipper Transcription FactorsGenes, ReporterTranscription Factor AP-2Chromatin ImmunoprecipitationLIM-Homeodomain ProteinsHeLa CellsKruppel-Like Transcription FactorsRecombinant Fusion ProteinsEnhancer Elements, GeneticTranscription Factors, TFIIGATA4 Transcription FactorProtein Structure, TertiaryCells, CulturedZinc FingersDrosophila ProteinsCloning, MolecularElectrophoretic Mobility Shift AssayYY1 Transcription FactorRegulatory Sequences, Nucleic AcidReverse Transcriptase Polymerase Chain ReactionSTAT3 Transcription FactorTranscription Factor TFIIDSequence Homology, Amino AcidActivating Transcription Factor 3NFATC Transcription FactorsSp3 Transcription FactorTranscription Initiation SiteNF-kappa BGene ExpressionDrosophilaGene Expression ProfilingPlasmidsActivating Transcription Factor 2Transcription Factor TFIIBIn Situ HybridizationOctamer Transcription Factor-1LuciferasesMEF2 Transcription FactorsE2F1 Transcription FactorRNA Polymerase IIGene Expression Regulation, FungalSequence AlignmentTCF Transcription FactorsBasic Helix-Loop-Helix Leucine Zipper Transcription FactorsConsensus SequenceConserved SequenceGATA3 Transcription FactorGene Expression Regulation, PlantGATA1 Transcription FactorPhenotypeProto-Oncogene ProteinsGATA2 Transcription FactorModels, BiologicalChromatinHelix-Loop-Helix MotifsGATA Transcription FactorsPhosphorylationSaccharomyces cerevisiaeMicrophthalmia-Associated Transcription FactorCell Line, TumorSaccharomyces cerevisiae ProteinsMice, KnockoutSTAT1 Transcription FactorActivating Transcription FactorsOligonucleotide Array Sequence AnalysisTwo-Hybrid System TechniquesTATA BoxBlotting, WesternTranscription Factor 7-Like 1 Protein
ProteinsProteinGenesPlant homeodomainLeucine zipperGenomeMotifsNucleotide sequencesMutationsSpecificityEncodesPost-transcriptional regulatoryEukaryoticMotifDevelopmentalGeneticSUPERFAMILYEvolutionarily conservedRegulationActivateInitiationAmino acidPromoterPlay important rolesWRKYSpecificYeastGene regulatoFamilyNuclearXenopusDomainMetabolismRoles in plant growthNext generationDifferentiation
Proteins12
Protein20
  • The small muscle-specific protein Csl modifies cell shape and promotes myocyte fusion in an insulin-like growth factor 1-dependent manner. (ox.ac.uk)
  • We have isolated a murine cDNA encoding a 9-kD protein, Chisel (Csl), in a screen for transcriptional targets of the cardiac homeodomain factor Nkx2-5. (ox.ac.uk)
  • Homeodomain-interacting protein kinases (HIPKs) belong to the CMGC kinase family and are closely related to dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs). (nature.com)
  • Homeodomain-interacting protein kinases (HIPKs) are an evolutionarily conserved kinase family comprising the members HIPK1, HIPK2, and HIPK3 in vertebrates, and, additionally, HIPK4 in mammals. (nature.com)
  • Plaza S., Prince F., Adachi Y., Punzo C., Cribbs D., Gehring W.J. Cross-regulatory Protein-Protein Interactions between Hox and Pax Transcription factors. (umassmed.edu)
  • The protein encoded by this gene is a mitogen-inducible monokine and is one of the major HIV-suppressive factors produced by CD8+ T-cells. (cancerindex.org)
  • We demonstrate here that GSK-3 maintains the MLL leukemia stem cell transcriptional program by promoting the conditional association of CREB and its coactivators TORC and CBP with homedomain protein MEIS1, a critical component of the MLL-subordinate program, which in turn facilitates HOX-mediated transcription and transformation. (stanford.edu)
  • Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. (embl.de)
  • Antennapedia homeodomain protein. (lookformedical.com)
  • Antennapedia homeodomain protein is a homeobox protein involved in limb patterning in ARTHROPODS. (lookformedical.com)
  • Mutations in the gene for the antennapedia homeodomain protein are associated with the conversion of antenna to leg or leg to antenna DROSOPHILA. (lookformedical.com)
  • A homeobox (HB) encodes a protein domain, the homeodomain (HD), which is a conserved 60-amino acid motif present in transcription factors found in all the eukaryotic organisms. (gao-lab.org)
  • The protein encoded by this gene is a DNA binding homeobox transcription factor involved in embryonic stem (ES) cell proliferation, renewal, and pluripotency. (nih.gov)
  • NRL interacts with homeodomain protein CRX and numerous other regulatory factors to control expression of most rod-expressed genes. (nih.gov)
  • First, the general TFs (GTFs), including preinitiation complex components TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and THIIH, are the primary protein factors that are required for the initiation of transcription from the TATA box (or TATA element), then elongation is executed by RNA polymerase II (RNA pol II) [ 1 ]. (intechopen.com)
  • Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for STB5 . (yeastrc.org)
  • Lactose regulatory protein LAC9 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / N. (yeastrc.org)
  • The reverse activity transcribes the ZAR2 mRNA with 966 nt coding sequence which codes for a 321 amino acid protein. (biomedcentral.com)
  • HD-Zip protein usually contain two highly conserved domains: homeodomain (HD) and leucine zipper (LZ) [ 1 ]. (biomedcentral.com)
  • The CDK4-cyclinD complex normally phosphorylates the retinoblastoma protein (Rb protein), leading to release of the E2F transcription factor and cell cycle progression. (medscape.com)
Genes18
  • Based on previous phylogenetic analyses in arabidopsis ( Arabidopsis thaliana ), our results showed that some tomato SL-ZH ( S. lycopersicum zinc-finger homeodomain) genes cluster into the same neighbor-joining (NJ) branch as arabidopsis, indicating that these genes may share similar structures and functions in these plants. (ashs.org)
  • TFs contain motifs for activation or repression of target genes through direct binding to gene regulatory elements or motifs. (ashs.org)
  • One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune . (nature.com)
  • For example, the AS-C transcription factors activate transcription of other genes, while the transcription factors of the E(spl)-C repress transcription. (sdbonline.org)
  • Developmental signals received by the Notch receptor cause Suppressor of Hairless (Su[H]) to mediate transcription of target genes. (sdbonline.org)
  • All three genes depend on Su(H) for initiation and/or maintenance of transcription. (sdbonline.org)
  • The expression patterns suggest that both genes are under the same regulatory control as are the E(spl) bHLH genes and thus, might play a part in Notch mediated cell differentiation. (sdbonline.org)
  • This mechanism also applies to hematopoietic cells transformed by other HOX genes, including CDX2, which is highly expressed in a majority of acute myeloid leukemias, thus providing a molecular approach based on GSK-3 inhibitory strategies to target HOX-associated transcription in a broad spectrum of leukemias. (stanford.edu)
  • Genes that encode highly conserved TRANSCRIPTION FACTORS that control positional identity of cells (BODY PATTERNING) and MORPHOGENESIS throughout development. (lookformedical.com)
  • Their sequences contain a 180 nucleotide sequence designated the homeobox, so called because mutations of these genes often results in homeotic transformations, in which one body structure replaces another. (lookformedical.com)
  • Within the Arabidopsis genome, 1,533 genes were found to encode members of known transcription factor families, 45% of which are from families specific for plants. (biomedcentral.com)
  • The fraction of transcription factor genes among all genes is slightly higher in Arabidopsis (5.9%) compared with Drosophila , C. elegans and yeast (4.5, 3.5 and 3.5%, respectively). (biomedcentral.com)
  • The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. (nih.gov)
  • Many vertebrate homeo box-containing genes have been identified on the basis of their sequence similarity with Drosophila developmental genes. (thermofisher.com)
  • We then surveyed the distribution of stress-related cis -regulatory elements in the −1.5 kb promoter regions of ZmCAMTA genes. (frontiersin.org)
  • Eighty known hearing loss genes were selected and simultaneously sequenced by targeted next-generation sequencing (NGS) in 8 Korean families with autosomal dominant non-syndromic sensorineural hearing loss. (biomedcentral.com)
  • Due to the limitation of the Sanger sequencing method, which is highly expensive and time-consuming, it has been difficult to sequence the hundreds of genes in these candidate chromosomal loci. (biomedcentral.com)
  • Therefore, based on the hypothesis that causative mutations of hearing loss are more likely to exist in known hearing loss associated-genes than in novel genes, we performed exon capture and resequencing using Illumina library generation and Solexa sequencing methods. (biomedcentral.com)
Plant homeodomain1
Leucine zipper2
  • A variety of prominent transcription factor families are present in all four species, including Myb, basic helix-loop-helix, basic leucine zipper, C2H2 zinc finger and homeodomain transcription factors. (biomedcentral.com)
  • These 23 PpHDZ transcription factors all contained a homeomorphism box domain and a leucine zipper domain, were divided into 4 subfamilies(I-IV) according to the evolutionary analysis, and their promoters contained many different cis-acting elements. (biomedcentral.com)
Genome6
  • Cancer genome sequencing reveals diverse acquired mutations in CTCF , which we have shown, functions as a tumour suppressor gene. (preprints.org)
  • The recent completion of the Arabidopsis thaliana genome sequence allowed the first prediction of a full plant proteome. (biomedcentral.com)
  • With the completed genome sequences of Saccharomyces cerevisiae (budding yeast), Caenorhabditis elegans and Drosophila melanogaster , complete proteomes from representatives of three eukaryotic kingdoms (plants, fungi and animals) are now available for comprehensive comparative studies. (biomedcentral.com)
  • Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. (biomedcentral.com)
  • The homeobox transcription factor HOXC13 upregulates human papillomavirus E1 gene expression and contributes to viral genome maintenance. (nih.gov)
  • However, the molecular mechanisms by which Otx and other transcription factors (TFs) interact with the genome to direct head formation are largely unknown. (xenbase.org)
Motifs2
  • Furthermore, in transcripts of both Brd and m4 there are three common regulatory sequence motifs within the 3' UTR. (sdbonline.org)
  • There are many superfamilies of Znf motifs, varying in both sequence and structure. (embl.de)
Nucleotide sequences2
  • Transcription factors (TFs), which bind to specific nucleotide sequences, have been shown to play important roles in the regulatory networks of numerous developmental processes in plants. (ashs.org)
  • Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)
Mutations1
  • Therefore, it has been nearly impossible to identify the precise pathogenic mutations in affected individuals from small families who cannot be examined either through linkage analysis or standard capillary sequencing analysis. (biomedcentral.com)
Specificity4
  • We have performed comprehensive analysis of homeodomain and Cys2His2 zinc finger specificities in D. melanogaster - (fruit fly) in collaboration with Michael Brodsky (UMMS-MCCB) & Gary Stormo (Wash. U). We have coupled this data with specificity data from artificial zinc fingers and homeodomains that we have selected using our bacterial one-hybrid system. (umassmed.edu)
  • Using this information we can build simple qualitative models of recognition that allow the design of homeodomains with novel DNA-binding specificity. (umassmed.edu)
  • This dataset can also be used to broadly predict the specificity of homeodomains ( http://stormo.wustl.edu/flyhd/ ) and zinc fingers ( http://stormo.wustl.edu/ZFModels/ ). (umassmed.edu)
  • Our findings establish Sox17 as a tissue -specific modifier of Wnt responses and point to a novel paradigm where genomic specificity of Wnt/β-catenin transcription is determined through functional interactions between lineage-specific Sox TFs and β-catenin/Tcf transcriptional complexes. (xenbase.org)
Encodes1
  • LMX1B encodes a LIM-homeodomain transcription factor. (nih.gov)
Post-transcriptional regulatory2
  • Since then, they have been found to be involved in the regulation of cell proliferation, migration and apoptosis as important post-transcriptional regulatory factors [ 15 ]. (ersjournals.com)
  • This project seeks to elucidate transcriptional and post-transcriptional regulatory networks that determine cell fate and guide the development of photoreceptors from retinal progenitor cells. (nih.gov)
Eukaryotic4
  • A comparative study based on four fully sequenced eukaryotic genomes has revealed profound differences in the sets of transcription factors used by plants, fungi and animals. (biomedcentral.com)
  • Both similarities and profound differences were revealed between the sets of transcription factors utilized by representatives of each eukaryotic kingdom. (biomedcentral.com)
  • These regulators, which constitute the largest class of plant transcription factors, are only weakly represented in the other eukaryotic kingdoms. (biomedcentral.com)
  • Nonetheless, this study reveals striking differences in the regulatory machineries utilized by three different eukaryotic kingdoms. (biomedcentral.com)
Motif1
  • As in m4 , the sequence motif of the Brd box is found twice in the 3'-UTR of malpha mRNA at similar positions but without a GY box. (sdbonline.org)
Developmental5
  • We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). (preprints.org)
  • Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism. (lookformedical.com)
  • Given that transcription factors act as central regulators of a diversity of developmental and physiological processes, such differences may partly account for the evolutionary distance between these entirely different life forms. (biomedcentral.com)
  • In particular, the existence of a great variety of transcription factors that are unique to distinct kingdoms, such as the large plant-specific AP2/EREBP and WRKY families and the animal-specific nuclear hormone receptors, reflects the need for specific solutions that meet the regulatory challenges connected with entirely different developmental programs and life styles. (biomedcentral.com)
  • The differential regulation of aos and btd domains by dri occurs at a time when Dri is found in all somatic nuclei of the embryo, so that Dri must be acting to permit the proper function of other developmental regulatory factors. (sdbonline.org)
Genetic3
  • Asthma is a complex and heterogeneous airway disease caused by genetic, environmental and epigenetic factors treated with hormones and biologics. (ersjournals.com)
  • Our understanding of the landscape of pediatric cancer genomics has improved markedly in the past 20 years with the advent of next generation sequencing and other high throughput genetic sequencing. (medscape.com)
  • This research holds great potential for elucidating how genetic variation and regulatory elements lead to diverse visual phenotypes. (nih.gov)
SUPERFAMILY1
Evolutionarily conserved1
Regulation3
  • Recombinant HIPKs and DYRK1A are auto-activated and phosphorylate the negative elongation factor SPT5, the transcription factor c-Myc, and the C-terminal domain of RNA polymerase II, suggesting a direct function in transcriptional regulation. (nature.com)
  • Further, we found that BMP-6 inhibited δEF1 transcription, resulting in an up-regulation of E-cadherin mRNA expression. (biomedcentral.com)
  • CCCTC-binding factor (CTCF) is a conserved transcription factor that performs diverse roles in transcriptional regulation and chromatin architecture. (preprints.org)
Activate2
  • We identified several LMX1B binding sites in the putative regulatory regions of both CD2AP and NPHS2 (podocin) and demonstrated that LMX1B binds to these sequences in vitro and can activate transcription through them in cotransfection assays. (nih.gov)
  • In some cases, Sox17 and β-catenin synergistically activate transcription apparently independent of Tcfs, whereas on other enhancers, Sox17 represses β-catenin/Tcf-mediated transcription to spatially restrict gene expression domains. (xenbase.org)
Initiation1
  • Molecular mechanisms of the initiation of transcription from TATA box have been well known as the most essential nuclear events in mammalian cells. (intechopen.com)
Amino acid2
  • Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. (embl.de)
  • This 60-amino acid sequence folds into a characteristic three-helix structure that is able to interact specifically with DNA. (gao-lab.org)
Promoter1
  • In addition to down-regulating the expression of δEF1, BMP-6 also physically dislodged δEF1 from E-cadherin promoter to allow the activation of E-cadherin transcription. (biomedcentral.com)
Play important roles1
WRKY1
  • As well as several small families, the large families of AP2/EREBP, NAC and WRKY transcription factors, consisting of 144, 109 and 72 members, respectively, are found exclusively in plants. (biomedcentral.com)
Specific12
  • Finally, the expression patterns of three neuronal type-specific transcription factors, unc-3, unc-4 and unc-30 , were altered. (biologists.com)
  • Our data suggest that cnd-1 may specify the identity of ventral cord motor neurons both by maintaining the mitotic competence of their precursors and by modulating the expression of neuronal type-specific determination factors. (biologists.com)
  • Hafler B.P., Surzenko N., Beier K.T., Punzo C ., Trimarchi J.M., Kong J.H., Cepko C.L. (2012) Transcription factor Olig2 defines subpopulations of retinal progenitor cells biased toward specific cell fates. (umassmed.edu)
  • This study characterized the canopy-layer specific transcriptome of five sorghum genotypes using RNA sequencing. (biomedcentral.com)
  • The expression systems are developed by cloning in the specific antibody DNA sequences from immunoreactive rabbits. (thermofisher.com)
  • Recent global analyses of gene transcripts revealed that specific transcription factors (TFs) and their networking systems physiologically correspond to the onset of human diseases, including cancer. (intechopen.com)
  • These different actions must depend on the combination of regulators acting on the respective position-specific cis-regulatory sequences. (sdbonline.org)
  • 2014), Occupancy of tissue-specific cis-regulatory mod. (xenbase.org)
  • Occupancy of tissue -specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification. (xenbase.org)
  • Here we employ ChIP-seq and RNA-seq approaches in Xenopus tropicalis gastrulae and find that occupancy of the corepressor, TLE/Groucho, is a better indicator of tissue -specific cis-regulatory modules (CRMs) than the coactivator p300 , during early embryonic stages. (xenbase.org)
  • HD-Zips (Homeodomain-Leucine Zippers) are a class of plant-specific transcription factors that play multiple roles in plant growth and development. (biomedcentral.com)
  • And the arrangement of the three helices determines the difference in the specific binding of homeodomain to DNA. (biomedcentral.com)
Yeast1
  • We show here that the PHD finger activates transcription in yeast, plant and animal cells. (gao-lab.org)
Gene regulato1
Family5
  • Members of the zinc-finger homeodomain (ZF-HD) family play a key role in the control of plant growth and development, which are involved in plant responses to stress. (ashs.org)
  • Within the HIPK family, HIPK1 and HIPK2 are the most closely related members, sharing about 93% sequence identity in their kinase domains, while HIPK3 is slightly less conserved with 87% identity. (nature.com)
  • The most divergent member of the family is HIPK4, which shares only 50% sequence identity with the catalytic domains of the three other HIPKs. (nature.com)
  • Except for the conserved DNA-binding domains, however, there are no significant similarities between members of the same transcription factor family from different kingdoms. (biomedcentral.com)
  • We previously discovered that that Maf-family bZIP transcription factor NRL is critical for rod photoreceptor fate and functional differentiation, and that loss of NRL leads to S-cones instead of rods. (nih.gov)
Nuclear4
  • The activities of transcription factors nuclear factor of activated T cells (NFAT) and myocyte enhancer-binding factor (MEF)2, were also enhanced in an IGF-1 signaling-dependent manner. (ox.ac.uk)
  • Hepatocyte Nuclear Factors" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (umassmed.edu)
  • This graph shows the total number of publications written about "Hepatocyte Nuclear Factors" by people in this website by year, and whether "Hepatocyte Nuclear Factors" was a major or minor topic of these publications. (umassmed.edu)
  • Below are the most recent publications written about "Hepatocyte Nuclear Factors" by people in Profiles. (umassmed.edu)
Xenopus1
Domain3
  • In accordance with the close relationship between HIPKs and other DYRK subfamily members, DYRK1A, a class I DYRK member, shares a sequence identity with HIPK3 of 38% within the catalytic domain. (nature.com)
  • and domain shuffling, leading to new combinations of common transcription factor domains. (biomedcentral.com)
  • The homeodomain domain is generally composed of about 60 amino acids encoded homeobox, which form three alpha helices. (biomedcentral.com)
Metabolism1
  • As a unique transcription factor in plants, HD-Zip plays an important regulatory role in plant growth and development, environmental response, cell cycle and cell metabolism [ 9 ]. (biomedcentral.com)
Roles in plant growth1
  • The calmodulin-binding transcription activators (CAMTA) play critical roles in plant growth and responses to environmental stimuli. (frontiersin.org)
Next generation2
  • We are using state-of-the-art next generation sequencing combined with bioinformatic strategies, and developing stem cell-based approaches for gene therapy and drug discovery. (nih.gov)
  • Next-generation sequencing (NGS) can overcome these limitations through its ability to perform parallel sequencing of billions of nucleotides at a low cost and high speed[ 1 - 4 ]. (biomedcentral.com)
Differentiation1
  • The basic helix-loop-helix transcription factor NeuroD (Neurod1) has been implicated in neuronal fate determination, differentiation and survival. (biologists.com)