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Genes, HomeoboxHomeodomain ProteinsAntennapedia Homeodomain ProteinMolecular Sequence DataTranscription FactorsBase SequenceAmino Acid SequenceLIM-Homeodomain ProteinsGene Expression Regulation, DevelopmentalDNA-Binding ProteinsDNAPaired Box Transcription FactorsGenomic InstabilityBinding SitesRepressor ProteinsMutationTranscription, GeneticGenomicsCloning, MolecularPromoter Regions, GeneticDrosophila ProteinsSequence Homology, Amino AcidProtein BindingSequence Analysis, DNAProtein Structure, TertiaryGenomic LibraryPhylogenyComparative Genomic HybridizationNuclear ProteinsSequence AlignmentDrosophilaTrans-ActivatorsConserved SequenceMSX1 Transcription FactorPhenotypeChromosome MappingGenomeIn Situ HybridizationGenomic IslandsGene Expression RegulationDNA PrimersRecombinant Fusion ProteinsEvolution, MolecularPolymerase Chain ReactionCell LineDNA, ComplementaryOctamer Transcription Factor-1Multigene FamilyEmbryo, NonmammalianOtx Transcription FactorsRNA, MessengerNerve Tissue ProteinsTranscriptional ActivationSequence Homology, Nucleic AcidGoosecoid ProteinEye ProteinsModels, GeneticModels, MolecularGene Expression ProfilingBody PatterningDrosophila melanogasterTranscription Factor Pit-1Genome, HumanConsensus SequenceCell DifferentiationExonsGenome, BacterialOligonucleotide Array Sequence AnalysisEnhancer Elements, GeneticPOU Domain FactorsHost Cell Factor C1Genomic ImprintingIntronsNucleic Acid HybridizationTransfectionZebrafishTwo-Hybrid System TechniquesXenopus ProteinsHepatocyte Nuclear Factor 6Genetic VariationZebrafish ProteinsGene ExpressionGene LibraryGenes, ReporterFushi Tarazu Transcription FactorsCell NucleusGenes, InsectRestriction MappingSequence DeletionAnimals, Genetically ModifiedInsect HormonesRegulatory Sequences, Nucleic AcidMorphogenesisSpecies SpecificityGene DosageBlotting, SouthernEmbryo, MammalianModels, BiologicalSignal Transduction
TranscriptionalChromosomeProteinsDROSOPHILAProteinMutationsWhole-exomeGenes encodeEncodeTranscription factorGenomeSangerChromosomalGenomesLeucine zipperAnalysesRegulationMotifNucleicBindInteractionsGene expressionAnalysisAminoHomeoticMutationalSimilarityStructureValidateMotifsAutosomalRegionMiceFamiliesSubjectsSpecificNext generationHumansFamilySearchDevelopmentResultsFunctionPartialTechnologiesWild-typeStudy
Transcriptional6
  • Single-cell RNA-Seq reveals a highly coordinated transcriptional program in mouse germ cells during primordial follicle formation. (nih.gov)
  • Sox17 is a key transcriptional regulator of definitive endoderm development, and yet, its genomic targets remain largely uncharacterized. (xenbase.org)
  • 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)
  • Homeodomain proteins are conserved DNA-binding factors that are involved in the transcriptional regulation of key developmental processes. (embl.de)
  • The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. (embl-heidelberg.de)
  • Furthermore, Smad proteins, transcriptional effectors of TGF-β signaling, are co-expressed and physically interact in the basal ganglia with Dlx homeodomain transcription factors, which are critical regulators of the differentiation, migration and survival of telencephalic GABAergic neurons. (biomedcentral.com)
Chromosome1
  • Previously, we developed statistical tools to identify association between the sites of provirus establishment and chromosome marks - as determined by chromatin immuno-precipitation with massively parallel DNA sequencing (ChIPSeq) [ 18 , 19 ]. (biomedcentral.com)
Proteins13
DROSOPHILA4
  • 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)
  • Homeotic mutations in Drosophila can result in dramatic phenotypes that suggest the possibility for rapid morphological evolution, but dissection of the genetic pathway downstream of Ultrabithorax is beginning to reveal how wing morphology may have evolved by more gradual transformations. (lookformedical.com)
  • By using published DNA binding specificity data for five transcription factors active in the early Drosophila embryo, genomic regions containing unusually high concentrations of predicted binding sites were identified for these factors. (sdbonline.org)
  • The structures of the Drosophila Paired homodimer and the yeast a1/alpha2 heterodimer bound to DNA, along with a high-resolution study of a Drosophila eve-DNA complex, have deepened our understanding of how homeodomains locate their DNA targets. (embl.de)
Protein8
  • Interestingly, our previous studies revealed that the viral Np9 protein is an oncoprotein and potently activates a variety of pathways such as β-catenin, ERK, Akt and Notch1, and promotes the growth of human leukemia stem/progenitor cells [ 1 ]. (aging-us.com)
  • Given that we previously defined the viral np9 gene, which is aberrantly activated in human leukemia, as a potent oncogene [ 1 ], we next attempted to search for cellular homologs of the viral oncogene np9 in NCBI database by performing alignment using Np9 protein sequence. (aging-us.com)
  • Antennapedia homeodomain protein. (lookformedical.com)
  • Antennapedia homeodomain protein is a homeobox protein involved in limb patterning in ARTHROPODS. (lookformedical.com)
  • The absence of genomic resources renders the search for paralogous cuttlefish genes dependent upon the presence of highly conserved protein motifs within genes of interest, thus we used a degenerate primer strategy to isolate partial coding sequence from the conserved domains specific to these families. (europa.eu)
  • One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
  • NRL interacts with homeodomain protein CRX and numerous other regulatory factors to control expression of most rod-expressed genes. (nih.gov)
  • Four members of the mouse Dlx protein family (Dlx1, 2, 5 and 6), part of the Antennapedia class of non-Hox homeodomain transcription factors, are expressed in the embryonic subpallium (Panganiban and Rubenstein 2002 ). (biomedcentral.com)
Mutations6
  • Understanding the mutations in NOBOX homeodomain is important to researchers and clinicians to develop diagnostic and therapeutic approaches for POF such as genetic control of mammalian reproductive life-span, regulation of fertility, and generation of mature eggs in the lab. (wikipedia.org)
  • 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)
  • PCR and Sanger sequencing were used to confirm mutations in and screen other family members where they were available. (molvis.org)
  • Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations. (embl.de)
  • 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)
  • 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)
Whole-exome1
  • performed whole-exome sequencing in a Palestinian family with hereditary hearing loss and identified a novel mutation in the gene, GPSM2 , which had been hidden in the autosomal recessive hearing loss locus (DFNB32) first identified by Masmoudi et al. (biomedcentral.com)
Genes encode1
  • The genes encode homeodomain-containing transcription factors that control cell fates by regulating the transcription of downstream target genes. (nih.gov)
Encode1
  • The PITX gene encode the paired-like homeodomain transcription factor family. (nature.com)
Transcription factor2
  • Orthologous to human PHTF1 (putative homeodomain transcription factor 1). (nih.gov)
  • Putative homeodomain transcription factor 1 interacts with the feminization factor homolog fem1b in male germ cells. (nih.gov)
Genome4
  • Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. (nature.com)
  • A major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. (sdbonline.org)
  • PWMs are a useful way to represent binding specificities and provide a statistical framework for searching for novel instances of the motif in genome sequences (Berman, 2002). (sdbonline.org)
  • molecular studies are difficult due to the absence of genome sequence data for any cephalopod. (europa.eu)
Sanger5
  • BACKGROUND: Sanger dideoxy sequencing is vital in clinical analysis due to its accuracy, ability to analyze genetic markers like SNPs and STRs, capability to generate reliable DNA profiles, and its role in resolving complex clinical cases. (bvsalud.org)
  • The precision and robustness of Sanger sequencing contribute significantly to the scientific basis of clinical investigations. (bvsalud.org)
  • SHORT CONCLUSION: This overview sheds light on prominent technical concerns that can emerge prior to and during the interpretation of DNA chromatograms in Sanger sequencing, along with offering strategies to address them effectively. (bvsalud.org)
  • Recognizing these concerns can aid in enhancing the quality of downstream analyses for Sanger sequencing results, which holds notable improvement in accuracy, reliability, and ability to provide crucial genetic information in clinical analysis. (bvsalud.org)
  • 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)
Chromosomal2
  • Characterization of the chromosomal rearrangements shown in Figure 1 also revealed that two genetic elements (proximal and distal MES [maintenance elements for silencing]), about 70 kb apart in the Scr gene, must be in cis to maintain proper repression. (nih.gov)
  • The transcription units are shown above the genomic DNA, while chromosomal aberrations are shown below (solid triangles indicate insertions of transposable elements and upward arrows indicate breakpoints of translocations and inversions). (nih.gov)
Genomes2
  • Here, we sequence the genomes of Aurelia aurita (a scyphozoan) and Morbakka virulenta (a cubozoan) to understand the molecular mechanisms responsible for the origin of the jellyfish body plan. (oist.jp)
  • Vertebrate genomes contain retroviral sequences that are believed to be remnants of exogenous retroviral infection from the distant past [ 1 ]. (biomedcentral.com)
Leucine zipper1
  • 2000). "The leucine zipper of NRL interacts with the CRX homeodomain. (en-academic.com)
Analyses2
  • To ensure the accuracy of DNA sequencing outcomes, it is also imperative to detect and rectify technical challenges that may lead to misinterpretation of the DNA sequence, resulting in errors and incongruities in subsequent analyses. (bvsalud.org)
  • 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)
Regulation3
  • Regulation of these oocyte-specific genes is thru direct binding of NOBOX to its promoter regions via the specific consensus sequences, the NOBOX DNA binding elements (NBEs). (wikipedia.org)
  • Regulation of actin dynamics and analysis of genomic influences on actin function. (upstate.edu)
  • A comparison of wild type and two Aa ttg1 alleles revealed that Aa TTG1 is involved in the regulation of all five traits. (biomedcentral.com)
Motif2
  • The binding sequences for each factor were aligned by using the motif-assembly program, and the binding specificities of each factor were modeled with position weight matrices (PWMs). (sdbonline.org)
  • Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. (embl.de)
Nucleic2
  • Thus, it is not feasible to read nucleic acid sequences without giving serious attention to these technical problems. (bvsalud.org)
  • The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. (lookformedical.com)
Bind1
  • Past structural studies have focused on the binding of monomeric homeodomains to DNA, but two recent structures have revealed how homeodomains bind DNA as multimers. (embl.de)
Interactions1
  • Homeodomain interactions. (embl.de)
Gene expression3
  • Relative levels of gene expression throughout development were determined by quantitative polymerase chain reaction (PCR) analysis and in cases where sufficient specific gene sequence was acquired, ribonucleic acid (RNA) probes were generated to evaluate the spatial expression patterns during the period of organogenesis. (europa.eu)
  • The gene expression before and after Wnt activation is compared within each intestinal origin and across the three locations using RNA sequencing. (biomedcentral.com)
  • The rapid improvement of descriptive genomic technologies has fueled a dramatic increase in hypothesized connections between cardiovascular gene expression and phenotypes. (mdpi.com)
Analysis2
  • Spatial expression analysis of both genes revealed that Sof-RXR is expressed ubiquitously in all cells of the embryo, including the chondrocytes, whereas Sof-ALDH was expressed only in a sub-set of epithelial cells and no expression at the level of chondrocytes was observed. (europa.eu)
  • 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences" . (en-academic.com)
Amino3
  • Homeodomain is a stretch of 32 specific amino acids in primates downstream the NOBOX Arg303 residue and is very well-conserved among the species. (wikipedia.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)
  • 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-heidelberg.de)
Homeotic1
  • The changes provide powerful assays for identifying the trans -acting factors that regulate the homeotic genes and the cis -acting sequences through which they act. (nih.gov)
Mutational1
Similarity1
  • The solution structure of the Oct-1 POU-specific domain reveals a striking similarity to the bacteriophage lambda repressor DNA-binding domain. (embl.de)
Structure2
  • It was then cloned and characterised for its genomic structure. (wikipedia.org)
  • There are many superfamilies of Znf motifs, varying in both sequence and structure. (embl-heidelberg.de)
Validate1
Motifs1
  • The full-length p200 isoform contains four DNA binding motifs, three CUT repeats, and a homeodomain. (nature.com)
Autosomal1
  • 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)
Region2
  • Using CIS-ANALYST, the distribution of Bcd, Cad, Hb, Kr, and Kni binding sites were examined in a 1-Mb genomic region surrounding the well-characterized eve locus at a site_p value of 0.0003. (sdbonline.org)
  • Each of these domains contains a helical region resembling the homeodomain and the Hin recombinase. (embl.de)
Mice2
  • Knockout study of NOBOX against wild-type ovaries in newborn female mice revealed that 74% (28/38 genes) were downregulated more than 5-fold and 15% (5/33 genes) were upregulated more than 5-fold. (wikipedia.org)
  • In the study of genomic cis -regulatory elements, generation of mice featuring transgenic reporters or cis -regulatory element knockout remains the standard approach. (mdpi.com)
Families1
  • By comparison with DNA sequences from exogenous retrovirus families, three main classes of HERVs, gamma, beta, and delta have been identified [ 2 ]. (biomedcentral.com)
Subjects1
  • In the current study, a total of 279 unrelated subjects ascertained for ASDs were screened for genomic disorders associated with CI using MLPA. (biomedcentral.com)
Specific2
  • The POU-specific (POUs) domain, in association with a POU-type homeodomain, forms the bipartite DNA-binding POU domain. (embl.de)
  • This study characterized the canopy-layer specific transcriptome of five sorghum genotypes using RNA sequencing. (biomedcentral.com)
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)
Humans1
Family1
  • Exome sequencing was performed in one affected family member. (molvis.org)
Search1
  • It is one of the several genes that appeared in the search in expressed sequence tag (EST) databases of mouse. (wikipedia.org)
Development1
  • Our goal is to understand how linear information encoded in genomic DNA controls cell fates during development. (nih.gov)
Results1
  • Our studies also identify some limitations of MLPA, where single base changes in probe binding sequences alter results. (biomedcentral.com)
Function1
  • Moreover, its significant negative effect suggests that NOBOX homeodomain may function as a dimer but its rare occurrence suggests a low contribution to POF. (wikipedia.org)
Partial1
  • We isolated partial coding sequence for a retinoid X receptor (RXR) receptor (Sof-RXR : JN101950) and an aldehyde dehydrogenase (ALDH) (Sof-ALDH : JN101949) homologue. (europa.eu)
Technologies1
  • We use cutting-edge genomic technologies, and focus on RNA biology and proteomics. (nih.gov)
Wild-type1
  • A detailed microscopic investigation has revealed how wild-type fungal hyphae, of the sequenced strain PH-1, colonised susceptible wheat ears and spread from spikelet to spikelet. (rothamsted.ac.uk)
Study1
  • A study conducted on 96 white women with POF revealed one case of heterozygous mutation in the NOBOX homeodomain, p.Arg355His, in one patient. (wikipedia.org)