regulator genes

Summary

Summary: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.

Top Publications

  1. Miele A, Dekker J. Long-range chromosomal interactions and gene regulation. Mol Biosyst. 2008;4:1046-57 pubmed publisher
    ..Finally, we propose that a genome-wide network analysis may provide new insights into the logic of long-range gene regulation. ..
  2. Chen H, Lin A, Bloom J, Khan A, Park C, Smith D. Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 allele-dependent APOE coding region enhancer. Genomics. 2008;92:292-300 pubmed publisher
    ..Our results suggest a wider variety of mammalian transcriptional regulatory sequences than is currently recognized and that these may include coding region SNPs. ..
  3. Ghai V, Gaudet J. The CSL transcription factor LAG-1 directly represses hlh-6 expression in C. elegans. Dev Biol. 2008;322:334-44 pubmed publisher
    ..We also identify an additional cis-regulatory element in the hlh-6 promoter that, together with previously identified elements, is sufficient to overcome repression by LAG-1 and activate hlh-6 expression in pharyngeal glands. ..
  4. O Meara M, Bigelow H, Flibotte S, Etchberger J, Moerman D, Hobert O. Cis-regulatory mutations in the Caenorhabditis elegans homeobox gene locus cog-1 affect neuronal development. Genetics. 2009;181:1679-86 pubmed publisher
    ..The multiplicity of cis-regulatory elements may ensure the robustness of gene expression. ..
  5. Bailey T, Boden M, Buske F, Frith M, Grant C, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37:W202-8 pubmed publisher
    ..All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net. ..
  6. Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res. 2008;36:5221-31 pubmed publisher
    ..Using tag density as an indicator of DNA-binding affinity, we have identified core residues within the NRSF and CTCF binding sites that are critical for a stronger DNA binding. ..
  7. Tuteja G, Jensen S, White P, Kaestner K. Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site. Nucleic Acids Res. 2008;36:4149-57 pubmed publisher
    ..We not only provide a better understanding of the mechanisms of Foxa2 regulation but also introduce a novel method for identification of different cis-regulatory modules involving a single factor. ..
  8. Blahnik K, Dou L, O Geen H, McPhillips T, Xu X, Cao A, et al. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 2010;38:e13 pubmed publisher
    ..We demonstrate the utility of our software by collecting, analyzing and comparing ChIP-seq data for six different human transcription factors/cell line combinations. ..
  9. Heintzman N, Ren B. Finding distal regulatory elements in the human genome. Curr Opin Genet Dev. 2009;19:541-9 pubmed publisher
    ..Here, we review these advances, focusing on two important classes of distal regulatory sequences-enhancers and insulators. ..

More Information

Publications62

  1. Lamber E, Vanhille L, Textor L, Kachalova G, Sieweke M, Wilmanns M. Regulation of the transcription factor Ets-1 by DNA-mediated homo-dimerization. EMBO J. 2008;27:2006-17 pubmed publisher
    ..Our findings may also explain previous data of Ets-1 function in the context of heterologous transcription factors, thus providing a molecular model that could also be valid for Ets-1 regulation by hetero-oligomeric assembly. ..
  2. Ling G, Sugathan A, Mazor T, Fraenkel E, Waxman D. Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. Mol Cell Biol. 2010;30:5531-44 pubmed publisher
    ..This approach can readily be applied to mapping condition-specific regulatory sites in mammalian tissues under a wide variety of physiological conditions. ..
  3. Boden M, Bailey T. Associating transcription factor-binding site motifs with target GO terms and target genes. Nucleic Acids Res. 2008;36:4108-17 pubmed publisher
    ..Results on human reference sets are similarly encouraging. Validation of our target gene prediction method shows that its accuracy exceeds that of simple motif scanning. ..
  4. Kim N, Tharakaraman K, Mariño Ramírez L, Spouge J. Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. BMC Bioinformatics. 2008;9:262 pubmed publisher
  5. Thomas Chollier M, Sand O, Turatsinze J, Janky R, Defrance M, Vervisch E, et al. RSAT: regulatory sequence analysis tools. Nucleic Acids Res. 2008;36:W119-27 pubmed publisher
    ..Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published. ..
  6. Miura H, Tomaru Y, Nakanishi M, Kondo S, Hayashizaki Y, Suzuki M. Identification of DNA regions and a set of transcriptional regulatory factors involved in transcriptional regulation of several human liver-enriched transcription factor genes. Nucleic Acids Res. 2009;37:778-92 pubmed publisher
    ..Finally, co-transfection reporter assays with various combinations of expression vectors for these HNF genes demonstrated the transcriptional activation of the CEBPA gene in a combinatorial manner by these TRFs. ..
  7. Segal E, Widom J. From DNA sequence to transcriptional behaviour: a quantitative approach. Nat Rev Genet. 2009;10:443-56 pubmed publisher
    ..It can also be used to model more complex phenomena such as transcriptional noise and the evolution of transcriptional regulation. ..
  8. Wederell E, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, et al. Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res. 2008;36:4549-64 pubmed publisher
    ..Our comprehensive results for in vivo Foxa2-binding sites in the mouse liver will contribute to resolving transcriptional regulatory networks that are important for adult liver function. ..
  9. Wels M, Groot Kormelink T, Kleerebezem M, Siezen R, Francke C. An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters. BMC Genomics. 2008;9:330 pubmed publisher
    ..Furthermore, our analysis of the species-dependency of the occurrence of specific T-boxes indicated that these regulatory elements propagate in a semi-independent way from the genes that they control. ..
  10. Turatsinze J, Thomas Chollier M, Defrance M, van Helden J. Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc. 2008;3:1578-88 pubmed publisher
    ..This protocol is also tested on random control sequences to evaluate the reliability of the predictions. Each task requires a few minutes of computation time on the server. The complete protocol can be executed in about one hour. ..
  11. Fauteux F, Blanchette M, Stromvik M. Seeder: discriminative seeding DNA motif discovery. Bioinformatics. 2008;24:2303-7 pubmed publisher
    ..The algorithm is applied to the analysis of plant tissue-specific promoter sequences and successfully identifies key regulatory elements. ..
  12. Kimura N, Takamatsu N, Yaoita Y, Osamura R, Kimura N. Identification of transcriptional regulatory elements in the human somatostatin receptor sst2 promoter and regions including estrogen response element half-site for estrogen activation. J Mol Endocrinol. 2008;40:75-91 pubmed publisher
    ..The present results should provide a molecular basis for transcriptional regulation in a variety of physiological and pathological contexts of sst2-expressing tissues. ..
  13. Kim B, Kim W, Park D, Chung W, Shin K, Bhak J. SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions. BMC Bioinformatics. 2008;9 Suppl 1:S2 pubmed publisher
    ..It was created in order to predict functional SNPs in putative promoter regions and predicted transcription factor binding sites. SNP@Promoter will help researchers to identify functional SNPs in non-coding regions. ..
  14. Rada Iglesias A, Ameur A, Kapranov P, Enroth S, Komorowski J, Gingeras T, et al. Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res. 2008;18:380-92 pubmed publisher
    ..This expands our understanding about the transcriptional control of metabolic processes and its alteration in metabolic disorders. ..
  15. Manke T, Roider H, Vingron M. Statistical modeling of transcription factor binding affinities predicts regulatory interactions. PLoS Comput Biol. 2008;4:e1000039 pubmed publisher
    ..Its successful application to human promoter sequences serves as an encouraging example of how the method can be applied to other sequences. ..
  16. Noyes M, Meng X, Wakabayashi A, Sinha S, Brodsky M, Wolfe S. A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res. 2008;36:2547-60 pubmed publisher
  17. Gan X, Wang J, Xi Y, Wu Z, Li Y, Li L. Nuclear Dvl, c-Jun, beta-catenin, and TCF form a complex leading to stabilization of beta-catenin-TCF interaction. J Cell Biol. 2008;180:1087-100 pubmed publisher
    ..Our results reveal a mechanism by which nuclear Dvl cooperates with c-Jun to regulate gene transcription stimulated by the canonical Wnt signaling pathway. ..
  18. Nakanishi M, Tomaru Y, Miura H, Hayashizaki Y, Suzuki M. Identification of transcriptional regulatory cascades in retinoic acid-induced growth arrest of HepG2 cells. Nucleic Acids Res. 2008;36:3443-54 pubmed publisher
    ..Finally, 36 transcriptional regulatory edges were validated by chromatin immunoprecipitation. These analyses enabled us to depict a part of the transcriptional regulatory cascades closely linked to ATRA-induced cell growth arrest. ..
  19. Warner J, Philippakis A, Jaeger S, He F, Lin J, Bulyk M. Systematic identification of mammalian regulatory motifs' target genes and functions. Nat Methods. 2008;5:347-53 pubmed publisher
    ..This approach is general and can be applied readily to any cell type, gene expression pattern or organism of interest. ..
  20. Astanehe A, Arenillas D, Wasserman W, Leung P, Dunn S, Davies B, et al. Mechanisms underlying p53 regulation of PIK3CA transcription in ovarian surface epithelium and in ovarian cancer. J Cell Sci. 2008;121:664-74 pubmed publisher
  21. Gotea V, Ovcharenko I. DiRE: identifying distant regulatory elements of co-expressed genes. Nucleic Acids Res. 2008;36:W133-9 pubmed publisher
    ..Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. The DiRE web server is freely available at http://dire.dcode.org. ..
  22. Yang Y, Song E, Kim E, Lee K, Kim W, Park S, et al. NdgR, an IclR-like regulator involved in amino-acid-dependent growth, quorum sensing, and antibiotic production in Streptomyces coelicolor. Appl Microbiol Biotechnol. 2009;82:501-11 pubmed publisher
    ..These results suggest a global regulatory role for NdgR in amino acid metabolisms, quorum sensing, morphological changes, antibiotic production, and expression of chaperonines in S. coelicolor. ..
  23. Yoon H, McDermott J, Porwollik S, McClelland M, Heffron F. Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium. PLoS Pathog. 2009;5:e1000306 pubmed publisher
    ..Furthermore, experiments to demonstrate epistatic relationships showed that SsrB can replace SlyA and, in some cases, SlyA can replace SsrB for expression of SPI-2 encoded virulence factors...
  24. Krueger K, Deneris E. Serotonergic transcription of human FEV reveals direct GATA factor interactions and fate of Pet-1-deficient serotonin neuron precursors. J Neurosci. 2008;28:12748-58 pubmed publisher
    ..Our findings identify a direct transcriptional interaction between Gata-2 and FEV and a unique marker for new insight into FEV/Pet-1 function in 5-HT neuron development. ..
  25. Bamne M, Talkowski M, Chowdari K, Nimgaonkar V. Functional analysis of upstream common polymorphisms of the dopamine transporter gene. Schizophr Bull. 2010;36:977-82 pubmed publisher
    ..We have thus identified novel putative regulatory domains flanking the core promoter of DAT that merit further investigation. ..
  26. Jnawali H, Lee H, Sohng J. Enhancement of clavulanic acid production by expressing regulatory genes in gap gene deletion mutant of Streptomyces clavuligerus NRRL3585. J Microbiol Biotechnol. 2010;20:146-52 pubmed
    ..24- and 6.51-fold in the pHN11 and pHN12 transformants, respectively, glycerol increased CA by 2.96- and 6.21-fold, respectively, and ornithine and glycerol together increased CA by 3.72- and 7.02-fold, respectively. ..
  27. Ohtomo T, Miyatake S, Kajiyama Y, Umezu Goto M, Kobayashi N, Kaminuma O, et al. Airway eosinophilic inflammation is attenuated in conserved noncoding sequence-1-deficient mice. Int Arch Allergy Immunol. 2008;146 Suppl 1:2-6 pubmed publisher
    ..When mice were sensitized with OVA/aluminum twice, induction of eosinophilia and OVA-specific IgE Ab was not significantly different between CNS-1-/- and CNS-1+/+ mice. CNS-1 locus regulates eosinophilic inflammation in vivo. ..
  28. Corcoran C, Dorman C. DNA relaxation-dependent phase biasing of the fim genetic switch in Escherichia coli depends on the interplay of H-NS, IHF and LRP. Mol Microbiol. 2009;74:1071-82 pubmed publisher
  29. Liu Y, Peacey E, Dickson J, Donahue C, Zheng S, Varani G, et al. Mitoxantrone analogues as ligands for a stem-loop structure of tau pre-mRNA. J Med Chem. 2009;52:6523-6 pubmed publisher
    ..These findings establish essential structure-activity relationships to further optimize the activity of this promising class of compounds. ..
  30. Onodera T, Sakai T, Hsu J, Matsumoto K, Chiorini J, Yamada K. Btbd7 regulates epithelial cell dynamics and branching morphogenesis. Science. 2010;329:562-5 pubmed publisher
    ..Inhibition experiments show that Btbd7 is required for branching of embryonic mammalian salivary glands and lungs. Hence, Btbd7 is a regulatory gene that promotes epithelial tissue remodeling and formation of branched organs. ..
  31. Bodson M, Breuskin I, Lefebvre P, Malgrange B. Hair cell progenitors: identification and regulatory genes. Acta Otolaryngol. 2010;130:312-7 pubmed publisher
    ..Characterization of signals that maintain, expand and regulate these progenitors will be essential for the biomedical application of stem cell populations to restore hearing. ..
  32. Wang J, Bowen N, Mariño Ramírez L, Jordan I. A c-Myc regulatory subnetwork from human transposable element sequences. Mol Biosyst. 2009;5:1831-9 pubmed publisher
    ..These data point to a substantial contribution of TEs to the regulation of human genes by c-Myc. Genes that are regulated by TE-derived c-Myc binding sites appear to form a distinct c-Myc regulatory subnetwork. ..
  33. Heinz S, Benner C, Spann N, Bertolino E, Lin Y, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576-89 pubmed publisher
  34. Bhat Nakshatri P, Wang G, Collins N, Thomson M, Geistlinger T, Carroll J, et al. Estradiol-regulated microRNAs control estradiol response in breast cancer cells. Nucleic Acids Res. 2009;37:4850-61 pubmed publisher
    ..Additionally, our studies reveal a negative-regulatory loop controlling E2 response through microRNAs as well as differences in E2-induced transcriptome and proteome. ..
  35. Stedman A, Lecaudey V, Havis E, Anselme I, Wassef M, Gilardi Hebenstreit P, et al. A functional interaction between Irx and Meis patterns the anterior hindbrain and activates krox20 expression in rhombomere 3. Dev Biol. 2009;327:566-77 pubmed publisher
    ..Together, our data point to an essential function of Iroquois transcription factors in krox20 activation and, more generally, in anterior hindbrain specification. ..
  36. Belogurov G, Sevostyanova A, Svetlov V, Artsimovitch I. Functional regions of the N-terminal domain of the antiterminator RfaH. Mol Microbiol. 2010;76:286-301 pubmed publisher
    ..The third region is apparently dispensable for RfaH binding to the transcription complex but is required for the antitermination modification of RNAP. ..
  37. Sholtis S, Noonan J. Gene regulation and the origins of human biological uniqueness. Trends Genet. 2010;26:110-8 pubmed publisher
    ..Although the evolutionary interpretation of these events is a subject of considerable debate, the technical and analytical means are now at hand to identify the set of evolutionary genetic events that shaped our species. ..
  38. Marui J, Ohashi Kunihiro S, Ando T, Nishimura M, Koike H, Machida M. Penicillin biosynthesis in Aspergillus oryzae and its overproduction by genetic engineering. J Biosci Bioeng. 2010;110:8-11 pubmed publisher
    ..Overexpression of the biosynthetic genes by a strong promoter yielded a greater than 100-fold increase in penicillin production. ..
  39. Chang S, Brown C. Identification of regulatory elements flanking human XIST reveals species differences. BMC Mol Biol. 2010;11:20 pubmed publisher
  40. Hellen C. IRES-induced conformational changes in the ribosome and the mechanism of translation initiation by internal ribosomal entry. Biochim Biophys Acta. 2009;1789:558-70 pubmed publisher
  41. Lee J, Park I, Gao Y, Li J, Li Z, Daley G, et al. A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet. 2009;5:e1000718 pubmed publisher
    ..We show that our approach to mapping cis-regulatory variants reduces in vitro experimental noise and reveals additional tissue-specific variants using skin-derived human iPS cells. ..
  42. Munitic I, Evaristo C, Sung H, Rocha B. Transcriptional regulation during CD8 T-cell immune responses. Adv Exp Med Biol. 2010;684:11-27 pubmed
    ..These modifications are the consequence of changes in the expression of multiple genes, i.e., on the utilization of a new transcription program. ..
  43. Skowronska Krawczyk D, Chiodini F, Ebeling M, Alliod C, Kundzewicz A, Castro D, et al. Conserved regulatory sequences in Atoh7 mediate non-conserved regulatory responses in retina ontogenesis. Development. 2009;136:3767-77 pubmed publisher
    ..In summary, we show how highly conserved regulatory elements are put to use in mediating non-conserved functions and creating interspecies neuronal diversity. ..
  44. Kraus D, Herbert S, Kristian S, Khosravi A, Nizet V, G tz F, et al. The GraRS regulatory system controls Staphylococcus aureus susceptibility to antimicrobial host defenses. BMC Microbiol. 2008;8:85 pubmed publisher
    ..aureus in a mouse infection model. Our results indicate that S. aureus can regulate its surface properties in order to overcome innate host defenses...
  45. Renzi F, Rescalli E, Galli E, Bertoni G. Identification of genes regulated by the MvaT-like paralogues TurA and TurB of Pseudomonas putida KT2440. Environ Microbiol. 2010;12:254-63 pubmed publisher
    ..In addition, our results indicate that TurA is the master regulator of TurB as well as of the other paralogues, TurD and TurE. ..
  46. Milan D, Kim A, Winterfield J, Jones I, Pfeufer A, Sanna S, et al. Drug-sensitized zebrafish screen identifies multiple genes, including GINS3, as regulators of myocardial repolarization. Circulation. 2009;120:553-9 pubmed publisher
    ..Among these genes is GINS3, the human ortholog of which is a major locus in 2 concurrent human genome-wide association studies of QT interval. These results reveal a novel network of genes that regulate cardiac repolarization. ..
  47. Dellarole M, Sánchez I, de Prat Gay G. Thermodynamics of cooperative DNA recognition at a replication origin and transcription regulatory site. Biochemistry. 2010;49:10277-86 pubmed publisher
    ..This is in surprising agreement with previous results for this domain, which revealed a strong coupling between global dynamics and DNA recognition. ..
  48. Tucker N, Le Brun N, Dixon R, Hutchings M. There's NO stopping NsrR, a global regulator of the bacterial NO stress response. Trends Microbiol. 2010;18:149-56 pubmed publisher
    ..Recent advances in biochemical and transcriptomic studies of NsrR make it timely to review the current evidence for NsrR as a global regulator and to speculate on the recent controversy over its NO sensing mechanism. ..
  49. Haddad Mashadrizeh A, Zomorodipour A, Izadpanah M, Sam M, Ataei F, Sabouni F, et al. A systematic study of the function of the human beta-globin introns on the expression of the human coagulation factor IX in cultured Chinese hamster ovary cells. J Gene Med. 2009;11:941-50 pubmed publisher
    ..The larger number of TFBs in the second hBG intron reflects its stronger effect. The results obtained suggest possible synergistic functions of the hBG introns and Kozak on the expression level of hFIX in vitro. ..
  50. Cooper M, Loose M, Brookfield J. The evolutionary influence of binding site organisation on gene regulatory networks. Biosystems. 2009;96:185-93 pubmed publisher
    ..Methods for the circumvention of these constraints, and the potential of the evolutionary modeling approach, are discussed. ..
  51. Zou X, Zhu Y, Pohlmann E, Li J, Zhang Y, Roberts G. Identification and functional characterization of NifA variants that are independent of GlnB activation in the photosynthetic bacterium Rhodospirillum rubrum. Microbiology. 2008;154:2689-99 pubmed publisher
    ..This suggests that the necessary alteration of the pool of effector(s) for NifA activation cannot be obtained by knockout mutations...
  52. Singh L, Hannenhalli S. Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families. Nucleic Acids Res. 2010;38:738-49 pubmed publisher
    ..Our work presents a novel means of investigating the cis regulatory changes potentially mediating expression divergence in paralogous gene families under specific conditions. ..
  53. Kang K, Chung J, Kim J. Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites. Nucleic Acids Res. 2009;37:2003-13 pubmed publisher
    ..Individual ChIP experiments confirmed the in vivo binding of the YY1 and CTCF proteins to most of these newly discovered binding sites, demonstrating the feasibility and usefulness of ECMFinder. ..