Functional evolution of the p53 regulatory network through its target response elements.

Abstract:

:Transcriptional network evolution is central to the development of complex biological systems. Networks can evolve through variation of master regulators and/or by changes in regulation of genes within networks. To gain insight into meaningful evolutionary differences in large networks, it is essential to address the functional consequences of sequence differences in response elements (REs) targeted by transcription factors. Using a combination of custom bioinformatics and multispecies alignment of promoter regions, we investigated the functional evolution of REs in terms of responsiveness to the sequence-specific transcription factor p53, a tumor suppressor and master regulator of stress responses. We identified REs orthologous to known p53 targets in human and rodent cells or alternatively REs related to the established p53 consensus. The orthologous REs were assigned p53 transactivation capabilities based on rules determined from model systems, and a functional heat map was developed to visually summarize conservation of sequence and relative level of responsiveness to p53 for 47 REs in 14 species. Individual REs exhibited marked differences in transactivation potentials and widespread evolutionary turnover. Functional differences were often not predicted from consensus sequence evaluations. Of the established human p53 REs analyzed, 91% had sequence conservation in at least one nonprimate species compared with 67.5% for functional conservation. Surprisingly, there was almost no conservation of functional REs for genes involved in DNA metabolism or repair between humans and rodents, suggesting important differences in p53 stress responses and cancer development.

authors

Jegga AG,Inga A,Menendez D,Aronow BJ,Resnick MA

doi

10.1073/pnas.0704694105

subject

Has Abstract

pub_date

2008-01-22 00:00:00

pages

944-9

issue

3

eissn

0027-8424

issn

1091-6490

pii

0704694105

journal_volume

105

pub_type

杂志文章
  • Gene therapy with a single chain interleukin 12 fusion protein induces T cell-dependent protective immunity in a syngeneic model of murine neuroblastoma.

    abstract::A major goal of tumor immunotherapy is the effective eradication of established metastases associated with the induction of a T cell-mediated protective immunity. We achieved this in a poorly immunogenic murine neuroblastoma model by gene therapy with a single chain interleukin 12 (scIL-12) fusion protein that assures...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.5.2475

    authors: Lode HN,Dreier T,Xiang R,Varki NM,Kang AS,Reisfeld RA

    更新日期:1998-03-03 00:00:00

  • Homozygosity and patch structure in plant populations as a result of nearest-neighbor pollination.

    abstract::The population genetic consequences of nearest-neighbor pollination in an outcrossing plant species were investigated through computer simulations. The genetic system consisted of two alleles at a single locus in a self-incompatible plant that mates by random pollen transfer from a neighboring individual. Beginning wi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.79.1.203

    authors: Turner ME,Stephens JC,Anderson WW

    更新日期:1982-01-01 00:00:00

  • Curved DNA: design, synthesis, and circularization.

    abstract::Curved DNA molecules and unusually small circles have been obtained by ligation of synthetic 21-base precursors: (sequence in text). The ligation resulted in the formation of double-stranded oligo-(precursor)s possessing a strong 10.5-base-pair (bp) periodicity of the runs of adenines. Two-dimensional polyacrylamide g...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.4.862

    authors: Ulanovsky L,Bodner M,Trifonov EN,Choder M

    更新日期:1986-02-01 00:00:00

  • Exon shuffling generates an immunoglobulin heavy chain gene.

    abstract::From endonuclease EcoRI partial libraries of DNAs from mouse embryo and MOPC 141, a gamma 2b-producing myeloma, clones were isolated by using a DNA fragment carrying the gamma 2b constant (C) region gene as a hybridization probe. One clone from MOPC 141 contained a heavy chain variable (V) gene and the C gamma 2b gene...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.4.2138

    authors: Maki R,Traunecker A,Sakano H,Roeder W,Tonegawa S

    更新日期:1980-04-01 00:00:00

  • Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation.

    abstract::Rapid antibody production in response to invading pathogens requires the dramatic expansion of pathogen-derived antigen-specific B lymphocyte populations. Whether B cell population dynamics are based on stochastic competition between competing cell fates, as in the development of competence by the bacterium Bacillus s...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1715639115

    authors: Mitchell S,Roy K,Zangle TA,Hoffmann A

    更新日期:2018-03-20 00:00:00

  • Targeting AMAP1 and cortactin binding bearing an atypical src homology 3/proline interface for prevention of breast cancer invasion and metastasis.

    abstract::Invasive potentials of carcinomas greatly contribute to their metastasis, which is a major threat in most cancers. We have recently shown that Arf6 plays a pivotal role in breast cancer invasive activities and identified AMAP1 as an effector of GTP-Arf6 in invasion. Expression of AMAP1 correlates well with invasive ph...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0509166103

    authors: Hashimoto S,Hirose M,Hashimoto A,Morishige M,Yamada A,Hosaka H,Akagi K,Ogawa E,Oneyama C,Agatsuma T,Okada M,Kobayashi H,Wada H,Nakano H,Ikegami T,Nakagawa A,Sabe H

    更新日期:2006-05-02 00:00:00

  • Poly(A) binding protein abundance regulates eukaryotic translation initiation factor 4F assembly in human cytomegalovirus-infected cells.

    abstract::By commandeering cellular translation initiation factors, or destroying those dispensable for viral mRNA translation, viruses often suppress host protein synthesis. In contrast, cellular protein synthesis proceeds in human cytomegalovirus (HCMV)-infected cells, forcing viral and cellular mRNAs to compete for limiting ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1202829109

    authors: McKinney C,Perez C,Mohr I

    更新日期:2012-04-10 00:00:00

  • Pre-B cell receptor expression is necessary for thymic stromal lymphopoietin responsiveness in the bone marrow but not in the liver environment.

    abstract::IL-7 and thymic stromal lymphopoietin (TSLP) are two major cytokines controlling murine B cell development. IL-7 has been studied extensively, but only recently has it become possible to unravel the role of TSLP in detail. We studied the biological activities of TSLP in B cell development at distinct ages in the mouse...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0402919101

    authors: Vosshenrich CA,Cumano A,Müller W,Di Santo JP,Vieira P

    更新日期:2004-07-27 00:00:00

  • Correlation of song learning and territory establishment strategies in the song sparrow.

    abstract::In a field study, we show that a young song sparrow (i) selects his songs from three or four older birds who have neighboring territories, (ii) preferentially learns song types that these tutor neighbors share, and (iii) ultimately sets up his territory next to, or replaces, one of these tutor neighbors. The consequen...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.4.1450

    authors: Beecher MD,Campbell SE,Stoddard PK

    更新日期:1994-02-15 00:00:00

  • Elimination of zinc from synaptic vesicles in the intact mouse brain by disruption of the ZnT3 gene.

    abstract::The mammalian protein ZnT3 resides on synaptic vesicle membranes of zinc-containing neurons, suggesting its possible role in vesicular zinc transport. We show here that histochemically reactive zinc, corresponding to the zinc found within synaptic vesicles, was undetectable in the brains of mice with targeted disrupti...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.4.1716

    authors: Cole TB,Wenzel HJ,Kafer KE,Schwartzkroin PA,Palmiter RD

    更新日期:1999-02-16 00:00:00

  • Amino acid sequence of the heat-stable inhibitor of the cAMP-dependent protein kinase from rabbit skeletal muscle.

    abstract::The amino acid sequence of rabbit skeletal muscle heat-stable inhibitor of the cAMP-dependent protein kinase has been determined by microsequencing techniques. Proof of the structure involved a series of nonoverlapping tryptic fragments for primary identification of 86% of the amino acids. Complementary fragments gene...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.82.17.5732

    authors: Scott JD,Fischer EH,Takio K,Demaille JG,Krebs EG

    更新日期:1985-09-01 00:00:00

  • Reversible oxidation and inactivation of the tumor suppressor PTEN in cells stimulated with peptide growth factors.

    abstract::Stimulation of cells with various peptide growth factors induces the production of phosphatidylinositol 3,4,5-trisphosphate (PIP3) through activation of phosphatidylinositol 3-kinase. The action of this enzyme is reversed by that of the tumor suppressor PTEN. With the use of cells overexpressing NADPH oxidase 1 or per...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0407396101

    authors: Kwon J,Lee SR,Yang KS,Ahn Y,Kim YJ,Stadtman ER,Rhee SG

    更新日期:2004-11-23 00:00:00

  • Activation of human immunodeficiency virus by herpesvirus infection: identification of a region within the long terminal repeat that responds to a trans-acting factor encoded by herpes simplex virus 1.

    abstract::Herpes simplex virus 1 (HSV-1) infection induces transcription of the chloramphenicol acetyltransferase (CAT) gene directed by the long terminal repeat (LTR) of human immunodeficiency virus (HIV) in both transiently and permanently transfected cells containing the HIV-LTR/CAT hybrid gene. To define the mechanism by wh...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.84.21.7408

    authors: Mosca JD,Bednarik DP,Raj NB,Rosen CA,Sodroski JG,Haseltine WA,Hayward GS,Pitha PM

    更新日期:1987-11-01 00:00:00

  • Effect of pressure on the electronic structure of ferric hydroxamates and ferrichrome A.

    abstract::The effect of pressure up to 175 kilobars on the electronic structure of three ferric hydroxamates and on ferrichrome A has been studied by optical absorption and Mössbauer resonance. The ferric ion was reduced to ferrous ion with pressure, as has been previously observed for various compounds. For the hydroxamates, t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.68.3.549

    authors: Grenoble DC,Drickamer HG

    更新日期:1971-03-01 00:00:00

  • Loss of microRNA cluster miR-29a/b-1 in sporadic Alzheimer's disease correlates with increased BACE1/beta-secretase expression.

    abstract::Although the role of APP and PSEN genes in genetic Alzheimer's disease (AD) cases is well established, fairly little is known about the molecular mechanisms affecting Abeta generation in sporadic AD. Deficiency in Abeta clearance is certainly a possibility, but increased expression of proteins like APP or BACE1/beta-s...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0710263105

    authors: Hébert SS,Horré K,Nicolaï L,Papadopoulou AS,Mandemakers W,Silahtaroglu AN,Kauppinen S,Delacourte A,De Strooper B

    更新日期:2008-04-29 00:00:00

  • Disparate foundations of scientists' policy positions on contentious biomedical research.

    abstract::What drives scientists' position taking on matters where empirical answers are unavailable or contradictory? We examined the contentious debate on whether to limit experiments involving the creation of potentially pandemic pathogens. Hundreds of scientists, including Nobel laureates, have signed petitions on the debat...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1613580114

    authors: Edelmann A,Moody J,Light R

    更新日期:2017-06-13 00:00:00

  • Lack of aldose 1-epimerase in Hypocrea jecorina (anamorph Trichoderma reesei): a key to cellulase gene expression on lactose.

    abstract::The heterodisaccharide lactose (1,4-O-beta-D-galactopyranosyl-D-glucose) induces cellulase formation in the ascomycete Hypocrea jecorina (= Trichoderma reesei). Lactose assimilation is slow, and the assimilation of its beta-D-galactose moiety depends mainly on the operation of a recently described reductive pathway an...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0802789105

    authors: Fekete E,Seiboth B,Kubicek CP,Szentirmai A,Karaffa L

    更新日期:2008-05-20 00:00:00

  • Coherent delta-band oscillations between cortical areas correlate with decision making.

    abstract::Coherent oscillations in the theta-to-gamma frequency range have been proposed as a mechanism that coordinates neural activity in large-scale cortical networks in sensory, motor, and cognitive tasks. Whether this mechanism also involves coherent oscillations at delta frequencies (1-4 Hz) is not known. Rather, delta os...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1314681110

    authors: Nácher V,Ledberg A,Deco G,Romo R

    更新日期:2013-09-10 00:00:00

  • The wound repair response controls outcome to cutaneous leishmaniasis.

    abstract::Chronic microbial infections are associated with fibrotic and inflammatory reactions known as granulomas showing similarities to wound-healing and tissue repair processes. We have previously mapped three leishmaniasis susceptibility loci, designated lmr1, -2, and -3, which exert their effect independently of T cell im...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0505630102

    authors: Sakthianandeswaren A,Elso CM,Simpson K,Curtis JM,Kumar B,Speed TP,Handman E,Foote SJ

    更新日期:2005-10-25 00:00:00

  • IL-1 family members and STAT activators induce cytokine production by Th2, Th17, and Th1 cells.

    abstract::Expression of T1ST2, the IL-33R, by Th2 cells requires GATA3. Resting Th2 cells express little GATA3, which is increased by IL-33 and a STAT5 activator, in turn increasing T1ST2 from its low-level expression on resting Th2 cells. Th2 cells that have upregulated T1ST2 produce IL-13, but not IL-4, in response to IL-33 p...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0906988106

    authors: Guo L,Wei G,Zhu J,Liao W,Leonard WJ,Zhao K,Paul W

    更新日期:2009-08-11 00:00:00

  • Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors.

    abstract::Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2006684117

    authors: Michaels TCT,Šarić A,Meisl G,Heller GT,Curk S,Arosio P,Linse S,Dobson CM,Vendruscolo M,Knowles TPJ

    更新日期:2020-09-29 00:00:00

  • Topological mechanics of gyroscopic metamaterials.

    abstract::Topological mechanical metamaterials are artificial structures whose unusual properties are protected very much like their electronic and optical counterparts. Here, we present an experimental and theoretical study of an active metamaterial--composed of coupled gyroscopes on a lattice--that breaks time-reversal symmet...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1507413112

    authors: Nash LM,Kleckner D,Read A,Vitelli V,Turner AM,Irvine WT

    更新日期:2015-11-24 00:00:00

  • Transcriptome-wide analysis of blood vessels laser captured from human skin and chronic wound-edge tissue.

    abstract::Chronic wounds represent a substantial public health problem. The development of tools that would enable sophisticated scrutiny of clinical wound tissue material is highly desirable. This work presents evidence enabling rapid specific identification and laser capture of blood vessels from human tissue in a manner whic...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0706793104

    authors: Roy S,Patel D,Khanna S,Gordillo GM,Biswas S,Friedman A,Sen CK

    更新日期:2007-09-04 00:00:00

  • Aerial dispersal and drying of Peronospora tabacina conidia in tobacco shade tents.

    abstract::Blue mold of tobacco is caused by the fungus Peronospora tabacina. Its spores are released in the morning when the relative humidity falls, but they require free water for germination. Traditionally, the walls of the shade tents are raised to control the pathogen by drying leaves. We show that raising the walls does n...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.79.2.697

    authors: Aylor DE,Taylor GS

    更新日期:1982-01-01 00:00:00

  • Intramolecular interaction between phosphorylated tyrosine-783 and the C-terminal Src homology 2 domain activates phospholipase C-gamma1.

    abstract::Phospholipase C-gamma1 (PLC-gamma1) contains two tandem Src homology 2 (SH2) domains. The NH(2)-terminal SH2 domain has been known to mediate the binding of PLC-gamma1 to receptor protein tyrosine kinases, which then activate PLC-gamma1 via phosphorylation at Y783. We now show that the phosphorylated Y783 residue (pY7...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0409590102

    authors: Poulin B,Sekiya F,Rhee SG

    更新日期:2005-03-22 00:00:00

  • Two sodium-channel genes in Drosophila: implications for channel diversity.

    abstract::We describe two Drosophila melanogaster transcription units that are highly homologous to a rat Na+-channel cDNA. They appear to encode the major subunits of two distinct Na+-channel proteins. One of these maps to the second chromosome and is identical to a Na+-channel gene whose partial sequence has been previously r...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.6.2079

    authors: Ramaswami M,Tanouye MA

    更新日期:1989-03-01 00:00:00

  • Capture of flanking DNA by a P element in Drosophila melanogaster: creation of a transposable element.

    abstract::A 6.1-kilobase insertion into the rudimentary (r) gene was cloned and partially sequenced. The insertion consists of a 703-base-pair (bp) P element next to a 5.4-kilobase single-copy sequence. The normal position of the single-copy sequence is near the tip of the X chromosome. Upon insertion into the r gene, this chim...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.3.693

    authors: Tsubota SI,Huong DV

    更新日期:1991-02-01 00:00:00

  • The water footprint of humanity.

    abstract::This study quantifies and maps the water footprint (WF) of humanity at a high spatial resolution. It reports on consumptive use of rainwater (green WF) and ground and surface water (blue WF) and volumes of water polluted (gray WF). Water footprints are estimated per nation from both a production and consumption perspe...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1109936109

    authors: Hoekstra AY,Mekonnen MM

    更新日期:2012-02-28 00:00:00

  • Identification of a 1,25-dihydroxyvitamin D3-response element in the 5'-flanking region of the rat calbindin D-9k gene.

    abstract::The rat calbindin D-9k gene is transcriptionally regulated by 1,25-dihydroxyvitamin D3 in the intestine. We have examined the 5'-flanking region of this gene and identified a 1,25-dihydroxyvitamin D3-responsive element (DRE) between nucleotides -489 and -445. This element confers 1,25-dihydroxyvitamin D3 responsivenes...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.2.603

    authors: Darwish HM,DeLuca HF

    更新日期:1992-01-15 00:00:00

  • In vivo antagonism of a T cell response by an endogenously expressed ligand.

    abstract::3.L2 T cell receptor transgenic T cells are activated by the 64-76 peptide of the mouse hemoglobin d beta chain [Hb(64-76)], and their response is antagonized by the position 72 alanine substitution of this peptide (A72). To test the effect of this altered peptide ligand (APL) on 3.L2 T cell function in vivo, a transg...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.24.14332

    authors: Basu D,Williams CB,Allen PM

    更新日期:1998-11-24 00:00:00