Genomes and Genes
Experts and Doctors on genetic transcription in Durham, United States
Locale: Durham, United States
Topic: genetic transcription
- Wyckoff E, Hsieh T. Functional expression of a Drosophila gene in yeast: genetic complementation of DNA topoisomerase II. Proc Natl Acad Sci U S A. 1988;85:6272-6 pubmed....
- Johnson D, Ohtani K, Nevins J. Autoregulatory control of E2F1 expression in response to positive and negative regulators of cell cycle progression. Genes Dev. 1994;8:1514-25 pubmed....
- Gesty Palmer D, El Shewy H, Kohout T, Luttrell L. beta-Arrestin 2 expression determines the transcriptional response to lysophosphatidic acid stimulation in murine embryo fibroblasts. J Biol Chem. 2005;280:32157-67 pubmed..These data indicate that beta-arrestin 2 functions both to attenuate EGF receptor transactivation-dependent signaling and to promote a distinct subset of ERK1/2-mediated responses to LPA receptor activation. ..
- Slotkin T, Seidler F. Oxidative and excitatory mechanisms of developmental neurotoxicity: transcriptional profiles for chlorpyrifos, diazinon, dieldrin, and divalent nickel in PC12 cells. Environ Health Perspect. 2009;117:587-96 pubmed publisher..The combined use of cell cultures and microarrays points to specific end points that can distinguish similarities and disparities in the effects of diverse developmental neurotoxicants. ..
- Hauser M, Horrigan S, Salmikangas P, Torian U, Viles K, Dancel R, et al. Myotilin is mutated in limb girdle muscular dystrophy 1A. Hum Mol Genet. 2000;9:2141-7 pubmed..Myotilin is a sarcomeric protein that binds to alpha-actinin and is localized in the Z-line. The observed missense mutation does not disrupt binding to alpha-actinin. ..
- Carty S, Greenleaf A. Hyperphosphorylated C-terminal repeat domain-associating proteins in the nuclear proteome link transcription to DNA/chromatin modification and RNA processing. Mol Cell Proteomics. 2002;1:598-610 pubmed..We propose that the phosphoCTD of elongating RNA polymerase II is a major organizer of nuclear functions. ..
- Kuan C, Wakiya K, Dowell J, Herndon J, Reardon D, Graner M, et al. Glycoprotein nonmetastatic melanoma protein B, a potential molecular therapeutic target in patients with glioblastoma multiforme. Clin Cancer Res. 2006;12:1970-82 pubmed....
- Kwiek N, Thacker D, Datto M, Megosh H, Haystead T. PITK, a PP1 targeting subunit that modulates the phosphorylation of the transcriptional regulator hnRNP K. Cell Signal. 2006;18:1769-78 pubmed..Taken together, our findings provide a putative mechanism by which transcriptional activity of hnRNP K can be discretely controlled through the regulation of PP1 activity. ..
- Lazorchak A, Schlissel M, Zhuang Y. E2A and IRF-4/Pip promote chromatin modification and transcription of the immunoglobulin kappa locus in pre-B cells. Mol Cell Biol. 2006;26:810-21 pubmed..Finally, we provide genetic evidence in the mouse that E2A gene dosage can influence the development of pre-B cells during the phase of Igkappa gene activation. ..
- Guo H, Gao C, Mi Z, Wai P, Kuo P. Phosphorylation of Ser158 regulates inflammatory redox-dependent hepatocyte nuclear factor-4alpha transcriptional activity. Biochem J. 2006;394:379-87 pubmed..This pathway results in enhanced iNOS expression in hepatocytes exposed to pro-inflammatory cytokines and oxidative stress. ..
- Chen Y, Weeks J, Mortin M, Greenleaf A. Mapping mutations in genes encoding the two large subunits of Drosophila RNA polymerase II defines domains essential for basic transcription functions and for proper expression of developmental genes. Mol Cell Biol. 1993;13:4214-22 pubmed..The clustering of these mutations in each gene suggests that they define functional domains in each subunit whose alteration induces the mutant phenotype. ..
- Liu S, Guo R, Quarles L. Cloning and characterization of the proximal murine Phex promoter. Endocrinology. 2001;142:3987-95 pubmed..Our findings are consistent with the predominant expression of Phex in bone and cartilage. Additional studies will be needed to confirm the regulatory regions in the Phex promoter that function in a cell-restricted manner. ..
- Long T, Brady S, Benfey P. Systems approaches to identifying gene regulatory networks in plants. Annu Rev Cell Dev Biol. 2008;24:81-103 pubmed publisher..Emergent properties revealed by the use of these network models and perspectives on the future of systems biology are discussed. ..
- Waddell D, Liberati N, Guo X, Frederick J, Wang X. Casein kinase Iepsilon plays a functional role in the transforming growth factor-beta signaling pathway. J Biol Chem. 2004;279:29236-46 pubmed..These results suggest that CKIepsilon plays a ligand-dependent, differential, and dual regulatory role within the TGF-beta signaling pathway. ..
- Oliverio M, Kim H, Ito M, Le T, Audoly L, Best C, et al. Reduced growth, abnormal kidney structure, and type 2 (AT2) angiotensin receptor-mediated blood pressure regulation in mice lacking both AT1A and AT1B receptors for angiotensin II. Proc Natl Acad Sci U S A. 1998;95:15496-501 pubmed..These studies reaffirm and extend the importance of AT1 receptors to mediate physiological functions of the renin-angiotensin system. ..
- Wang W, Nahta R, Huper G, Marks J. TAFII70 isoform-specific growth suppression correlates with its ability to complex with the GADD45a protein. Mol Cancer Res. 2004;2:442-52 pubmed..GADD45a null cells are not subject to TAFII70 inhibition, further supporting the relevance of this interaction. ..
- Meloni A, Smith E, Nevins J. A mechanism for Rb/p130-mediated transcription repression involving recruitment of the CtBP corepressor. Proc Natl Acad Sci U S A. 1999;96:9574-9 pubmed..We propose that E2F-mediated repression involves at least two events, either the recruitment of a histone deacetylase or the recruitment of the CtIP/CtBP corepressor complex. ..
- Marshall H, Stamler J. Inhibition of NF-kappa B by S-nitrosylation. Biochemistry. 2001;40:1688-93 pubmed..Further, an increase in S-nitrosylated p50 was detected in cells, and the level was modulated by TNFalpha. Taken together, these data suggest that S-nitrosylation of p50 is a physiological mechanism of NF-kappaB regulation. ..
- Miller H, Saunders K, Tomaras G, Garcia Blanco M. Tat-SF1 is not required for Tat transactivation but does regulate the relative levels of unspliced and spliced HIV-1 RNAs. PLoS ONE. 2009;4:e5710 pubmed publisher..These new findings highlight a novel, post-transcriptional role for Tat-SF1 in the HIV-1 life cycle. ..
- Anderson K, Means R, Huang Q, Kemp B, Goldstein E, Selbert M, et al. Components of a calmodulin-dependent protein kinase cascade. Molecular cloning, functional characterization and cellular localization of Ca2+/calmodulin-dependent protein kinase kinase beta. J Biol Chem. 1998;273:31880-9 pubmed..The strict Ca2+ requirement of CaMKIV-dependent phosphorylation of cAMP response element-binding protein, is therefore controlled at the level of CaMKIV rather than CaMKK. ..
- Silverstone A, Ciampaglio C, Sun T. The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway. Plant Cell. 1998;10:155-69 pubmed..Because the rga mutation abolished the high level of expression of the GA biosynthetic gene GA4 in the ga1-3 mutant background, we conclude that RGA may also play a role in controlling GA biosynthesis. ..
- Dolinski K, Muir S, Cardenas M, Heitman J. All cyclophilins and FK506 binding proteins are, individually and collectively, dispensable for viability in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1997;94:13093-8 pubmed..We propose that each cyclophilin and FKBP instead regulates a restricted number of unique partner proteins that remain to be identified. ..
- Lu Y, Ratnakar P, Mohanty B, Bastia D. Direct physical interaction between DnaG primase and DnaB helicase of Escherichia coli is necessary for optimal synthesis of primer RNA. Proc Natl Acad Sci U S A. 1996;93:12902-7 pubmed..Thus, the physical interaction reported here appears to be physiologically significant. ..
- Hawwari A, Krangel M. Regulation of TCR delta and alpha repertoires by local and long-distance control of variable gene segment chromatin structure. J Exp Med. 2005;202:467-72 pubmed....
- Robson Dixon N, Garcia Blanco M. MAZ elements alter transcription elongation and silencing of the fibroblast growth factor receptor 2 exon IIIb. J Biol Chem. 2004;279:29075-84 pubmed..We propose that RNAPII pauses at the MAZ4 elements resulting in a change in the transcription elongation complex that influences alternative splicing decisions downstream. ..
- Domalik L, Chaplin D, Kirkman M, Wu R, Liu W, Howard T, et al. Different isozymes of mouse 11 beta-hydroxylase produce mineralocorticoids and glucocorticoids. Mol Endocrinol. 1991;5:1853-61 pubmed..abstract truncated at 250 words) ..
- Wang D, Amornsiripanitch N, Dong X. A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog. 2006;2:e123 pubmed....
- Rooney R, Raychaudhuri P, Nevins J. E4F and ATF, two transcription factors that recognize the same site, can be distinguished both physically and functionally: a role for E4F in E1A trans activation. Mol Cell Biol. 1990;10:5138-49 pubmed..We conclude that the DNA-binding specificity of E4F as well as the alterations in DNA-binding activity of E4F closely correlates with E1A stimulation of the E4 promoter. ..
- Fuhrman L, Goel A, Smith J, Shianna K, Aballay A. Nucleolar proteins suppress Caenorhabditis elegans innate immunity by inhibiting p53/CEP-1. PLoS Genet. 2009;5:e1000657 pubmed publisher..Since nucleoli and p53/CEP-1 are conserved, our results reveal an ancient immune mechanism by which the nucleolus may regulate immune responses against bacterial pathogens. ..
- Guo H, Mi Z, Kuo P. Characterization of short range DNA looping in endotoxin-mediated transcription of the murine inducible nitric-oxide synthase (iNOS) gene. J Biol Chem. 2008;283:25209-17 pubmed publisher..In this "simplified" model of murine iNOS promoter, numerous transcription factors recognize and bind to various response elements, but these locales do not equally contribute to iNOS gene transcription...
- Lin F, Barun S, Lutz C, Wang Y, Hosford D. Decreased (45)Ca(2)(+) uptake in P/Q-type calcium channels in homozygous lethargic (Cacnb4lh) mice is associated with increased beta3 and decreased beta4 calcium channel subunit mRNA expression. Brain Res Mol Brain Res. 1999;71:1-10 pubmed..Together, these findings indicate that a host of changes in VGCC subunit composition accompany reduced function of P/Q-type channels in homozygous lethargic mice. ..
- Fridell R, Fischer U, Luhrmann R, Meyer B, Meinkoth J, Malim M, et al. Amphibian transcription factor IIIA proteins contain a sequence element functionally equivalent to the nuclear export signal of human immunodeficiency virus type 1 Rev. Proc Natl Acad Sci U S A. 1996;93:2936-40 pubmed..Thus, this shared protein motif may play an analogous role in mediating the nuclear export of both late HIV-1 RNAs and 5S rRNA transcripts. ..
- Guo H, Marroquin C, Wai P, Kuo P. Nitric oxide-dependent osteopontin expression induces metastatic behavior in HepG2 cells. Dig Dis Sci. 2005;50:1288-98 pubmed..Enhanced expression of OPN in this setting is associated with increased in vitro cell adhesion and invasion. These data suggest that NO enhances HCC expression of OPN and, as a result, conveys a metastatic phenotype. ..
- Whitesides J, Hall M, Anchan R, LaMantia A. Retinoid signaling distinguishes a subpopulation of olfactory receptor neurons in the developing and adult mouse. J Comp Neurol. 1998;394:445-61 pubmed....
- Xu P, Schmechel D, Rothrock Christian T, Burkhart D, Qiu H, Popko B, et al. Human apolipoprotein E2, E3, and E4 isoform-specific transgenic mice: human-like pattern of glial and neuronal immunoreactivity in central nervous system not observed in wild-type mice. Neurobiol Dis. 1996;3:229-45 pubmed..This pattern of immunoreactivity is similar to that observed in nonhuman primates and man, and contrasts with the strictly glial staining pattern of normal rodents. ..
- Chen W, Hu L, Semenov M, Yanagawa S, Kikuchi A, Lefkowitz R, et al. beta-Arrestin1 modulates lymphoid enhancer factor transcriptional activity through interaction with phosphorylated dishevelled proteins. Proc Natl Acad Sci U S A. 2001;98:14889-94 pubmed....
- Pfenning A, Kim T, Spotts J, Hemberg M, Su D, West A. Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways. PLoS ONE. 2010;5:e10870 pubmed publisher..Together these data strongly support the characterization of CaRF as a unique transcription factor and provide the first insight into the program of CaRF-regulated transcription in neurons. ..
- Upton M, Chen J, Guilak F, Setton L. Differential effects of static and dynamic compression on meniscal cell gene expression. J Orthop Res. 2003;21:963-9 pubmed....
- Odom A, Stahlberg A, Wente S, York J. A role for nuclear inositol 1,4,5-trisphosphate kinase in transcriptional control. Science. 2000;287:2026-9 pubmed..Thus, the phospholipase C pathway produces multiple IP messengers that modulate distinct nuclear processes. The results reveal a direct mechanism by which activation of IP signaling may control gene expression. ..
- Misra U, Pizzo S. Ligation of cell surface GRP78 with antibody directed against the COOH-terminal domain of GRP78 suppresses Ras/MAPK and PI 3-kinase/AKT signaling while promoting caspase activation in human prostate cancer cells. Cancer Biol Ther. 2010;9:142-52 pubmed..We conclude that antibody directed against the COOH-terminal domain of GRP78 may prove useful as a pan suppressor of proliferative/survival signaling in cancer cells expressing GRP78 on their cell surface. ..
- Rogers K, Higgins P, Milla M, Phillips R, Horowitz J. DP-2, a heterodimeric partner of E2F: identification and characterization of DP-2 proteins expressed in vivo. Proc Natl Acad Sci U S A. 1996;93:7594-9 pubmed..Thus, we conclude that DP-2 encodes a set of structurally, and perhaps functionally, distinct proteins in vivo. ..
- Morisaki T, Sabina R, Holmes E. Adenylate deaminase. A multigene family in humans and rats. J Biol Chem. 1990;265:11482-6 pubmed..The conservation of nucleotide sequence and exon/intron boundaries in these two genes suggests they arose by duplication of a common primordial gene around 150 million years ago. ..
- Cai X, Schäfer A, Lu S, Bilello J, Desrosiers R, Edwards R, et al. Epstein-Barr virus microRNAs are evolutionarily conserved and differentially expressed. PLoS Pathog. 2006;2:e23 pubmed..Moreover, the differential regulation of EBV miRNA expression implies distinct roles during infection of different human tissues...
- Hjelmstad R, Bell R. sn-1,2-diacylglycerol choline- and ethanolaminephosphotransferases in Saccharomyces cerevisiae. Nucleotide sequence of the EPT1 gene and comparison of the CPT1 and EPT1 gene products. J Biol Chem. 1991;266:5094-103 pubmed....
- Gao C, Guo H, Mi Z, Grusby M, Kuo P. Osteopontin induces ubiquitin-dependent degradation of STAT1 in RAW264.7 murine macrophages. J Immunol. 2007;178:1870-81 pubmed..These are novel findings and define OPN as a unique and as yet, poorly characterized, transactivator of STAT1 degradation by the ubiquitin-proteasome system. ..
- Ni T, Corcoran D, Rach E, Song S, Spana E, Gao Y, et al. A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods. 2010;7:521-7 pubmed publisher..We demonstrated paired-end TSS analysis to be a powerful method to uncover the transcriptional complexity of eukaryotic genomes. ..
- Gaillard S, Dwyer M, McDonnell D. Definition of the molecular basis for estrogen receptor-related receptor-alpha-cofactor interactions. Mol Endocrinol. 2007;21:62-76 pubmed....
- Slotkin T, Seidler F. Protein kinase C is a target for diverse developmental neurotoxicants: transcriptional responses to chlorpyrifos, diazinon, dieldrin and divalent nickel in PC12 cells. Brain Res. 2009;1263:23-32 pubmed publisher..These results further show how combined use of cell cultures and microarray technology can guide future in vivo work on diverse developmental neurotoxicants. ..
- Long T, Tsukagoshi H, Busch W, Lahner B, Salt D, Benfey P. The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots. Plant Cell. 2010;22:2219-36 pubmed publisher..PYE and BTS expression is also tightly coregulated. We propose that interactions among PYE, PYE homologs, and BTS are important for maintaining iron homeostasis under low iron conditions. ..
- Chellappan S, Hiebert S, Mudryj M, Horowitz J, Nevins J. The E2F transcription factor is a cellular target for the RB protein. Cell. 1991;65:1053-61 pubmed....
- Venturi G, Conway R, Steeber D, Tedder T. CD25+CD4+ regulatory T cell migration requires L-selectin expression: L-selectin transcriptional regulation balances constitutive receptor turnover. J Immunol. 2007;178:291-300 pubmed....
- Amalfitano A, Parks R. Separating fact from fiction: assessing the potential of modified adenovirus vectors for use in human gene therapy. Curr Gene Ther. 2002;2:111-33 pubmed....
- Guardiola A, Yao T. Molecular cloning and characterization of a novel histone deacetylase HDAC10. J Biol Chem. 2002;277:3350-6 pubmed..Together, our results identify HDAC10 as a novel deacetylase with distinct structure, pharmacology and localization and further expand the complexity of the HDAC family. ..
- Ohtani K, DeGregori J, Nevins J. Regulation of the cyclin E gene by transcription factor E2F1. Proc Natl Acad Sci U S A. 1995;92:12146-50 pubmed..These results suggest the involvement of E2F1 and cyclin E in an autoregulatory loop that governs the accumulation of critical activities affecting the progression of cells through G1. ..
- Arevalo Rodriguez M, Heitman J. Cyclophilin A is localized to the nucleus and controls meiosis in Saccharomyces cerevisiae. Eukaryot Cell. 2005;4:17-29 pubmed..Our findings reveal a novel nuclear role for cyclophilin A in governing the transcriptional program required for the vegetative to meiotic developmental switch in budding yeast. ..
- Giangrande P, Zhu W, Schlisio S, Sun X, Mori S, Gaubatz S, et al. A role for E2F6 in distinguishing G1/S- and G2/M-specific transcription. Genes Dev. 2004;18:2941-51 pubmed....
- Lopes N, Gregg D, Vasudevan S, Hassanain H, Goldschmidt Clermont P, Kovacic H. Thrombospondin 2 regulates cell proliferation induced by Rac1 redox-dependent signaling. Mol Cell Biol. 2003;23:5401-8 pubmed..These results identify Rac-induced ROS as a new pathway involved in the regulation of TSP2 expression. ..
- Zhao X, Sternsdorf T, Bolger T, Evans R, Yao T. Regulation of MEF2 by histone deacetylase 4- and SIRT1 deacetylase-mediated lysine modifications. Mol Cell Biol. 2005;25:8456-64 pubmed..Our studies reveal a novel regulation of MEF2 transcriptional activity by two distinct classes of deacetylases that affect MEF2 sumoylation and acetylation. ..
- Lima B, LAM G, Xie L, Diesen D, Villamizar N, Nienaber J, et al. Endogenous S-nitrosothiols protect against myocardial injury. Proc Natl Acad Sci U S A. 2009;106:6297-302 pubmed publisher..These results suggest innovative approaches to modulate angiogenesis and preserve cardiac function. ..
- Li X, McDonnell D. The transcription factor B-Myb is maintained in an inhibited state in target cells through its interaction with the nuclear corepressors N-CoR and SMRT. Mol Cell Biol. 2002;22:3663-73 pubmed..Cumulatively, these findings suggest that the nuclear corepressors N-CoR and SMRT serve a previously unappreciated role as regulators of B-Myb transcriptional activity. ..
- Brown S, Zhang C, Chen A, Hsieh T. Structure of the Drosophila DNA topoisomerase I gene and expression of messages with different lengths in the 3' untranslated region. Gene. 1998;211:195-203 pubmed..No significant heterogeneity at the 5' end of the top1 transcripts is seen. Sequence searches have revealed a number of regulatory sequences for potential translational control in the 3' untranslated region. ..
- King P, Levine T, Fremeau R, Keene J. Mammalian homologs of Drosophila ELAV localized to a neuronal subset can bind in vitro to the 3' UTR of mRNA encoding the Id transcriptional repressor. J Neurosci. 1994;14:1943-52 pubmed..These findings are interpreted in light of recent studies in which mRNA 3' UTRs were found to be important for the regulation of cell growth and differentiation. ..