Regulatory Sequences, Nucleic Acid

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  Subject Areas on Research

  • 4.5 kb of the rat tyrosine hydroxylase 5' flanking sequence directs tissue specific expression during development and contains consensus sites for multiple transcription factors. 
  • A 30-kDa alternative translation product of the CCAAT/enhancer binding protein alpha message: transcriptional activator lacking antimitotic activity. 
  • A 40-kilodalton protein binds specifically to an upstream sequence element essential for muscle-specific transcription of the human myoglobin promoter. 
  • A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes. 
  • A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF. 
  • A cis-regulatory map of the Drosophila genome. 
  • A compendium of promoter-centered long-range chromatin interactions in the human genome. 
  • A genomic regulatory network for development. 
  • A human gamma globin gene variant binds SP1. 
  • A naturally occurring gamma globin gene mutation enhances SP1 binding activity. 
  • A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. 
  • A regulatory cascade of three homeobox genes, ceh-10, ttx-3 and ceh-23, controls cell fate specification of a defined interneuron class in C. elegans. 
  • A small regulatory element from chromosome 19 enhances liver-specific gene expression. 
  • A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. 
  • ATAC-ing the mechanisms of renin regulation. 
  • Adaptive sequence divergence forged new neurodevelopmental enhancers in humans. 
  • Allele-specific gene expression in a wild nonhuman primate population. 
  • Allelic diversity in the TGFB1 regulatory region: characterization of novel functional single nucleotide polymorphisms. 
  • An antitumor drug-induced topoisomerase cleavage complex blocks a bacteriophage T4 replication fork in vivo. 
  • An integrated encyclopedia of DNA elements in the human genome. 
  • Analysis of muscle creatine kinase regulatory elements in recombinant adenoviral vectors. 
  • Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory region. 
  • Angiotensin II can regulate gene expression by the AP-1 binding sequence via a protein kinase C-dependent pathway. 
  • Architecture of the human regulatory network derived from ENCODE data. 
  • BCR sequences essential for transformation by the BCR-ABL oncogene bind to the ABL SH2 regulatory domain in a non-phosphotyrosine-dependent manner. 
  • Basal and thyroid hormone receptor auxiliary protein-enhanced binding of thyroid hormone receptor isoforms to native thyroid hormone response elements. 
  • Brevetoxin-6 (PbTx-6), a nonaromatic marine neurotoxin, is a ligand of the aryl hydrocarbon receptor. 
  • CRISPR-based methods for high-throughput annotation of regulatory DNA. 
  • Car8 dorsal root ganglion expression and genetic regulation of analgesic responses are associated with a cis-eQTL in mice. 
  • Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci. 
  • Characterization and tissue expression of multiple triiodothyronine receptor-auxiliary proteins and their relationship to the retinoid X-receptors. 
  • Characterization of a zinc finger DNA-binding protein expressed specifically in Petunia petals and seedlings. 
  • Characterization of cis-regulatory elements controlling repo transcription in Drosophila melanogaster. 
  • Characterization of cis-regulatory regions responsible for developmental regulation of the gibberellin biosynthetic gene GA1 in Arabidopsis thaliana 
  • Characterization of the human Snrpn minimal promoter and cis elements within it. 
  • Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. 
  • Chromatin-bound p53 anchors activated Smads and the mSin3A corepressor to confer transforming-growth-factor-beta-mediated transcription repression. 
  • Cis-regulatory evolution of chalcone-synthase expression in the genus Arabidopsis. 
  • Cloning and sequence analysis of the human beta 1-adrenergic receptor 5'-flanking promoter region. 
  • Cloning of the promoter region of human endoglin, the target gene for hereditary hemorrhagic telangiectasia type 1. 
  • Cloning of zebrafish vsx1: expression of a paired-like homeobox gene during CNS development. 
  • Combining location and expression data for principled discovery of genetic regulatory network models. 
  • Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee. 
  • Comparative genomics and regulatory evolution: conservation and function of the Chs and Apetala3 promoters. 
  • Computational tools for understanding sequence variability in recombination signals. 
  • Control of meiotic recombination and gene expression in yeast by a simple repetitive DNA sequence that excludes nucleosomes. 
  • Cooperation between core binding factor and adjacent promoter elements contributes to the tissue-specific expression of interleukin-3. 
  • Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution 
  • Core and region-enriched networks of behaviorally regulated genes and the singing genome. 
  • Creation of an active estrogen-responsive element by a single base change in the flanking sequence of a cellular oncogene: a possible mechanism for hormonal carcinogenesis? 
  • DNA Sequence Constraints Define Functionally Active Steroid Nuclear Receptor Binding Sites in Chromatin. 
  • DNA methylation of imprinted gene control regions in the regression of low-grade cervical lesions. 
  • DNA regulatory sequences of the rat tyrosine hydroxylase gene direct correct catecholaminergic cell-type specificity of a human growth hormone reporter in the CNS of transgenic mice causing a dwarf phenotype. 
  • DNA-binding protein RAP1 stimulates meiotic recombination at the HIS4 locus in yeast. 
  • DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. 
  • DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. 
  • Decoding the role of regulatory element polymorphisms in complex disease. 
  • Defining functional DNA elements in the human genome. 
  • Definition of a FoxA1 Cistrome that is crucial for G1 to S-phase cell-cycle transit in castration-resistant prostate cancer. 
  • Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription. 
  • Developmental regulation of V(D)J recombination at the TCR alpha/delta locus. 
  • Direct regulation of beta3-integrin subunit gene expression by HOXA10 in endometrial cells. 
  • Discovering sequences with potential regulatory characteristics. 
  • Dissecting the regulatory architecture of gene expression QTLs. 
  • Distinct combinations of NF-kappa B subunits determine the specificity of transcriptional activation. 
  • Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism. 
  • Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. 
  • Enhancer-blocking activity within the DNase I hypersensitive site 2 to 6 region between the TCR alpha and Dad1 genes. 
  • Epstein-Barr virus induces global changes in cellular mRNA isoform usage that are important for the maintenance of latency. 
  • Erythroid AP-1/NF-E2 elements vary in their response to NF-E2. 
  • Eukaryotic mRNPs may represent posttranscriptional operons. 
  • Evolution of a malaria resistance gene in wild primates. 
  • Evolution. CNCing is believing. 
  • Exploiting expression patterns across multiple tissues to map expression quantitative trait loci. 
  • Expression of human vitamin D receptor in Saccharomyces cerevisiae. Purification, properties, and generation of polyclonal antibodies. 
  • Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. 
  • Fetal hemoglobin in sickle cell anemia: genome-wide association studies suggest a regulatory region in the 5' olfactory receptor gene cluster. 
  • FoxA2, Nkx2.2, and PDX-1 regulate islet beta-cell-specific mafA expression through conserved sequences located between base pairs -8118 and -7750 upstream from the transcription start site. 
  • Functional heterogeneity of mammalian TATA-box sequences revealed by interaction with a cell-specific enhancer. 
  • Gamma-globin gene promoter elements required for interaction with globin enhancers. 
  • Gene expression and adaptive noncoding changes during human evolution. 
  • Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis. 
  • Genetics. Enhancing gene regulation. 
  • Genome accessibility is widely preserved and locally modulated during mitosis. 
  • Genome-wide quantification of the effects of DNA methylation on human gene regulation. 
  • Genomewide meta-analysis identifies loci associated with IGF-I and IGFBP-3 levels with impact on age-related traits. 
  • Genomic approaches for understanding the genetics of complex disease. 
  • Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. 
  • Half-site arrangement of hybrid glucocorticoid and thyroid hormone response elements specifies thyroid hormone receptor complex binding to DNA and transcriptional activity. 
  • Heterodimerization among thyroid hormone receptor, retinoic acid receptor, retinoid X receptor, chicken ovalbumin upstream promoter transcription factor, and an endogenous liver protein. 
  • HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization. 
  • High level expression of a truncated chicken progesterone receptor in Escherichia coli. 
  • How petals change their spots: cis-regulatory re-wiring in Clarkia (Onagraceae). 
  • Human and mouse alpha-synuclein genes: comparative genomic sequence analysis and identification of a novel gene regulatory element. 
  • IL-1R signaling promotes STAT3 and NF-κB factor recruitment to distal cis-regulatory elements that regulate Il17a/f transcription. 
  • Identification and analysis of eukaryotic promoters: recent computational approaches. 
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. 
  • Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae. 
  • Identification and requirements of enhancers that direct gene expression during zebrafish fin regeneration. 
  • Identification and utilization of arbitrary correlations in models of recombination signal sequences. 
  • Identification of E2A target genes in B lymphocyte development by using a gene tagging-based chromatin immunoprecipitation system. 
  • Identification of Smoking-Associated Differentially Methylated Regions Using Reduced Representation Bisulfite Sequencing and Cell type-Specific Enhancer Activation and Gene Expression. 
  • Identification of a negative regulatory element involved in tissue-specific expression of mouse renin genes. 
  • Identification of an estrogen response element in the 3'-flanking region of the murine c-fos protooncogene. 
  • Identification of negative and positive regulatory elements in the human renin gene. 
  • Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral. 
  • Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. 
  • In vivo footprinting of the human alpha-globin locus upstream regulatory element by guanine and adenine ligation-mediated polymerase chain reaction. 
  • In vivo identification of a negative regulatory element in the mouse renin gene using direct gene transfer. 
  • Induction of protein secretory pathway is required for systemic acquired resistance. 
  • Induction of stress proteins in cultured myogenic cells. Molecular signals for the activation of heat shock transcription factor during ischemia. 
  • Inhibition of Rev activity and human immunodeficiency virus type 1 replication by antisense oligodeoxynucleotide phosphorothioate analogs directed against the Rev-responsive element. 
  • Interactions of estrogen- and thyroid hormone receptors on a progesterone receptor estrogen response element (ERE) sequence: a comparison with the vitellogenin A2 consensus ERE. 
  • Interleukin-3 expression by activated T cells involves an inducible, T-cell-specific factor and an octamer binding protein. 
  • Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription. 
  • Investigation of the basis of virulence in serotype A strains of Cryptococcus neoformans from apparently immunocompetent individuals. 
  • Iron-dependent regulation of the divalent metal ion transporter. 
  • Knock-in tagging in zebrafish facilitated by insertion into non-coding regions. 
  • Ligand-induced recruitment of a histone deacetylase in the negative-feedback regulation of the thyrotropin beta gene. 
  • Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip). 
  • Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. 
  • Maternal cadmium, iron and zinc levels, DNA methylation and birth weight. 
  • Meiosis-specific double-strand DNA breaks at the HIS4 recombination hot spot in the yeast Saccharomyces cerevisiae: control in cis and trans. 
  • Methylomics of gene expression in human monocytes. 
  • MicroRNAs preferentially target the genes with high transcriptional regulation complexity. 
  • Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. 
  • Molecular hallmarks of endogenous chromatin complexes containing master regulators of hematopoiesis. 
  • Molecular mechanics simulation of the interaction of estrogen receptor with estrogen regulatory element. 
  • Molecular mechanisms of dominant negative activity by nuclear hormone receptors. 
  • Molecular organization and alternative splicing in zipper, the gene that encodes the Drosophila non-muscle myosin II heavy chain. 
  • Multiple Functional Variants in cis Modulate PDYN Expression. 
  • Multiple potential regulatory elements in the 5' flanking region of the human alpha 1a-adrenergic receptor. 
  • Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. 
  • New techniques for DNA sequence classification. 
  • Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis. 
  • Novel estrogen response elements identified by genetic selection in yeast are differentially responsive to estrogens and antiestrogens in mammalian cells. 
  • Overexpression of RRE-derived sequences inhibits HIV-1 replication in CEM cells. 
  • Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. 
  • Phylogenetic footprint analysis of IGF2 in extant mammals. 
  • Postmitotic expression of ankyrinR and beta R-spectrin in discrete neuronal populations of the rat brain. 
  • Potential associations between severity of infection and the presence of virulence-associated genes in clinical strains of Staphylococcus aureus. 
  • Predicting cell-type-specific gene expression from regions of open chromatin. 
  • Prolactin can modulate CD4+ T-cell response through receptor-mediated alterations in the expression of T-bet. 
  • Rapid evolution of cis-regulatory sequences via local point mutations. 
  • Ras induces p21Cip1/Waf1 cyclin kinase inhibitor transcriptionally through Sp1-binding sites. 
  • Regulated expression of p18, a major phosphoprotein of leukemic cells. 
  • Regulated expression of the tyrosine hydroxylase gene by epidermal growth factor. 
  • Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing. 
  • Selective loss of a DNase I hypersensitive site upstream of the tyrosine aminotransferase gene in mice homozygous for lethal albino deletions. 
  • Sequence and chromosomal location of the I-309 gene. Relationship to genes encoding a family of inflammatory cytokines. 
  • Sequences within the coding regions of clotting factor VIII and CFTR block transcriptional elongation. 
  • Signatures of protein-DNA recognition in free DNA binding sites. 
  • Simian virus 40 (SV40) T antigen binds specifically to double-stranded DNA but not to single-stranded DNA or DNA/RNA hybrids containing the SV40 regulatory sequences. 
  • Site-specific RNA cleavage generates the 3' end of a poxvirus late mRNA. 
  • Social environment influences the relationship between genotype and gene expression in wild baboons. 
  • Structural determinants of insert retention of poliovirus expression vectors with recombinant IRES elements. 
  • Structure and regulation of the chicken erythroid delta-aminolevulinate synthase gene. 
  • Targeted deletion of 5'HS2 of the murine beta-globin LCR reveals that it is not essential for proper regulation of the beta-globin locus. 
  • The Drosophila Translational Control Element (TCE) is required for high-level transcription of many genes that are specifically expressed in testes. 
  • The ENCODE (ENCyclopedia Of DNA Elements) Project. 
  • The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity. 
  • The MotA protein from bacteriophage T4 contains two domains. Preliminary structural analysis by X-ray diffraction and nuclear magnetic resonance. 
  • The accessible chromatin landscape of the human genome. 
  • The evolutionary significance of cis-regulatory mutations. 
  • The human plasminogen activator inhibitor type I gene promoter targets to kidney. 
  • Three periods of regulatory innovation during vertebrate evolution. 
  • Tissue-specific genetic control of splicing: implications for the study of complex traits. 
  • Transcription factor AP-2 regulates human immunodeficiency virus type 1 gene expression. 
  • Transcription-dependent mobilization of nucleosomes at accessible TCR gene segments in vivo. 
  • Transcriptional regulation and the evolution of development. 
  • Transcriptional regulation of Src homology 2 domain-containing leukocyte phosphoprotein of 76 kDa: dissection of key promoter elements. 
  • Tumor necrosis factor-alpha stimulates the maturation of sterol regulatory element binding protein-1 in human hepatocytes through the action of neutral sphingomyelinase. 
  • Two genetic changes in cis-regulatory elements caused evolution of petal spot position in Clarkia. 
  • UACUAAC is the preferred branch site for mammalian mRNA splicing. 
  • Use of recombinant adenovirus for metabolic engineering of mammalian cells. 
  • VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma. 
  • Vascular endothelial growth factor up-regulates cyclooxygenase-2 expression in human endothelial cells. 
  • WT1 and DAX-1 inhibit aromatase P450 expression in human endometrial and endometriotic stromal cells. 
  • Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution. 
  • hnRNP H and hnRNP F complex with Fox2 to silence fibroblast growth factor receptor 2 exon IIIc. 
  • p45 NF-E2 regulates expression of thromboxane synthase in megakaryocytes. 
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  Keywords of People

  • Alberts, Susan C., Robert F. Durden Distinguished Professor of Biology, Duke Science & Society
  • Bennett, Vann, George Barth Geller Distinguished Professor of Molecular Biology, Duke Cancer Institute
  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Krangel, Michael S., George Barth Geller Distinguished Professor of Immunology, Integrative Immunobiology
  • Reddy, Timothy E, Associate Professor of Biostatistics & Bioinformatics,, Molecular Genetics and Microbiology
  • Tsalik, Ephraim, Adjunct Associate Professor in the Department of Medicine, Medicine, Infectious Diseases
  • Wray, Gregory Allan, Professor of Biology, Evolutionary Anthropology