Identification of phylogenetic footprints in primate tumor necrosis factor-alpha promoters.

Abstract:

:The human tumor necrosis factor-alpha (TNF-alpha) gene encodes a pleiotropic cytokine that plays a critical role in basic immunologic processes. To investigate the TNF-alpha regulatory region in the primate lineage, we isolated TNF-alpha promoters from representative great apes, Old World monkeys, and New World monkeys. We demonstrate that there is a nonuniform distribution of fixed human differences in the TNF-alpha promoter. We define a "fixed human difference" as a site that is not polymorphic in humans, but which differs in at least one of the seven primate sequences examined. Furthermore, we identify two human TNF-alpha promoter single nucleotide polymorphisms that are putative ancestral polymorphisms, because each of the human polymorphic nucleotides was found at the identical site in at least one of the other primate sequences. Strikingly, the largest conserved region among the primate species, a 69-nt "phylogenetic footprint," corresponds to a region of the human TNF-alpha promoter that forms the transcriptionally active nucleoprotein-DNA complex, essential for gene regulation. By contrast, other regions of the TNF-alpha promoter, which exhibit a high density of variable sites, are nonessential for gene expression, indicating that distinct TNF-alpha promoter regions have been subjected to different evolutionary constraints depending on their function. TNF-alpha is the first case in which a promoter region dissected by functional analyses can be correlated with nucleotide polymorphism and variability in primate lineages. The results suggest that patterns of polymorphism and divergence are likely to be useful in identifying candidate regions important for gene regulation in other immune-response genes.

authors

Leung JY,McKenzie FE,Uglialoro AM,Flores-Villanueva PO,Sorkin BC,Yunis EJ,Hartl DL,Goldfeld AE

doi

10.1073/pnas.97.12.6614

keywords:

subject

Has Abstract

pub_date

2000-06-06 00:00:00

pages

6614-8

issue

12

eissn

0027-8424

issn

1091-6490

pii

97/12/6614

journal_volume

97

pub_type

杂志文章
  • Mouse amyloid protein AA: Homology with nonimmunoglobulin protein of human and monkey amyloid substance.

    abstract::The major protein extracted from anyloid deposits induced in mice by injection of either Candida albicans cells or sodium caseinate was found to have chromatographic and electrophoretic properties and an amino-acid compostiion characteristic of the AA class of amyloid proteins. The homology of the mouse protein with 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.73.3.964

    authors: Eriksen N,Ericsson LH,Pearsall N,Lagunoff D,Benditt EP

    更新日期:1976-03-01 00:00:00

  • Regulatory and structural motifs of chicken gizzard myosin light chain kinase.

    abstract::The amino acid sequence for chicken smooth muscle myosin light chain kinase (smMLCK) was deduced from a full-length cDNA. This has allowed definition of both the complete sequence of the inactive 64-kDa proteolytic fragment, which contains the pseudosubstrate autoregulatory sequence, and of the active 61-kDa Ca2+/calm...

    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.87.6.2284

    authors: Olson NJ,Pearson RB,Needleman DS,Hurwitz MY,Kemp BE,Means AR

    更新日期:1990-03-01 00:00:00

  • Structure of toroidal DNA collapsed inside the phage capsid.

    abstract::The structure of DNA toroids made of individual DNA molecules of various lengths (3,000 to 55,000 bp) was studied, by using partially filled bacteriophage capsids in conjunction with cryoelectron microscopy. The tetravalent cation spermine was diffused through the capsid to condense the DNA under conditions that were ...

    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.0901240106

    authors: Leforestier A,Livolant F

    更新日期:2009-06-09 00:00:00

  • The thyroid hormone-induced tail resorption program during Xenopus laevis metamorphosis.

    abstract::Genes that are up- and down-regulated by thyroid hormone in the tail resorption program of Xenopus laevis have been isolated by a gene expression screen, sequenced, and identified in the GenBank data base. The entire program is estimated to consist of fewer than 35 up-regulated and fewer than 10 down-regulated genes; ...

    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.93.5.1924

    authors: Brown DD,Wang Z,Furlow JD,Kanamori A,Schwartzman RA,Remo BF,Pinder A

    更新日期:1996-03-05 00:00:00

  • Brain 5-HT deficiency increases stress vulnerability and impairs antidepressant responses following psychosocial stress.

    abstract::Brain serotonin (5-HT) deficiency and exposure to psychosocial stress have both been implicated in the etiology of depression and anxiety disorders, but whether 5-HT deficiency influences susceptibility to depression- and anxiety-like phenotypes induced by psychosocial stress has not been formally established. Most cl...

    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.1416866112

    authors: Sachs BD,Ni JR,Caron MG

    更新日期:2015-02-24 00:00:00

  • A subset of group A-like var genes encodes the malaria parasite ligands for binding to human brain endothelial cells.

    abstract::Cerebral malaria is the most deadly manifestation of infection with Plasmodium falciparum. The pathology of cerebral malaria is characterized by the accumulation of infected erythrocytes (IEs) in the microvasculature of the brain caused by parasite adhesins on the surface of IEs binding to human receptors on microvasc...

    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.1120461109

    authors: Claessens A,Adams Y,Ghumra A,Lindergard G,Buchan CC,Andisi C,Bull PC,Mok S,Gupta AP,Wang CW,Turner L,Arman M,Raza A,Bozdech Z,Rowe JA

    更新日期:2012-06-26 00:00:00

  • Hierarchical model of gene regulation by transforming growth factor beta.

    abstract::Transforming growth factor betas (TGF-betas) regulate key aspects of embryonic development and major human diseases. Although Smad2, Smad3, and extracellular signal-regulated kinase (ERK) mitogen-activated protein kinases (MAPKs) have been proposed as key mediators in TGF-beta signaling, their functional specificities...

    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.1834070100

    authors: Yang YC,Piek E,Zavadil J,Liang D,Xie D,Heyer J,Pavlidis P,Kucherlapati R,Roberts AB,Böttinger EP

    更新日期:2003-09-02 00:00:00

  • An intermediate complex in the dissociation of aspartate transcarbamylase.

    abstract::The multisubunit enzyme aspartate transcarbamylase consists of six copies of two types of polypeptide chains, catalytic (C) and regulatory (R). A complex formed by the partial dissociation of this enzyme has been isolated. This species, which has the structure C(6)R(4), is a likely intermediate in the stepwise dissoci...

    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.71.4.1351

    authors: Evans DR,Pastra-Landis SC,Lipscomb WN

    更新日期:1974-04-01 00:00:00

  • Effects of dialyzable transfer factor in patients with breast cancer.

    abstract::Five patients with advanced breast cancer were treated with pooled dialyzable transfer factor from healthy adult donors. The period of treatment ranged from 21 to 310 days, the total dose from 20 to 257 ml. Transfer factor did not elicit inflammatory or hypersensitivity reactions or detectable formation of antibody to...

    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.71.6.2319

    authors: Oettgen HF,Old LJ,Farrow JH,Valentine FT,Lawrence HS,Thomas L

    更新日期:1974-06-01 00:00:00

  • Diurnal and circadian variation of sleep and alertness in men vs. naturally cycling women.

    abstract::This study quantifies sex differences in the diurnal and circadian variation of sleep and waking while controlling for menstrual cycle phase and hormonal contraceptive use. We compared the diurnal and circadian variation of sleep and alertness of 8 women studied during two phases of the menstrual cycle and 3 women stu...

    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.1524484113

    authors: Boivin DB,Shechter A,Boudreau P,Begum EA,Ng Ying-Kin NM

    更新日期:2016-09-27 00:00:00

  • A theory of group selection.

    abstract::In organisms possessing a dispersal phase the processes of mating, competition, feeding, and predation are often carried out within "trait-groups," defined as populations enclosed in areas smaller than the boundaries of the deme. A simple model shows that this can lead to the selection of "altruistic" traits that favo...

    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.72.1.143

    authors: Wilson DS

    更新日期:1975-01-01 00:00:00

  • Overview of the most prevalent hypothalamus-specific mRNAs, as identified by directional tag PCR subtraction.

    abstract::We applied the directional tag PCR subtractive hybridization method to construct a rat hypothalamic cDNA library from which cerebellar and hippocampal sequences had been depleted, enriching 20-30-fold for sequences expressed selectively in the hypothalamus. We studied a sample of 94 clones selected for enrichment in 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.93.16.8733

    authors: Gautvik KM,de Lecea L,Gautvik VT,Danielson PE,Tranque P,Dopazo A,Bloom FE,Sutcliffe JG

    更新日期:1996-08-06 00:00:00

  • Phase identity of the maize leaf is determined after leaf initiation.

    abstract::The vegetative development of the maize shoot can be divided into juvenile and adult phases based on the types of leaves produced at different times in shoot development. Models for the regulation of phase change make explicit predictions about when the identity of these types of leaves is determined. To test these mo...

    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.180301597

    authors: Orkwiszewski JA,Poethig RS

    更新日期:2000-09-12 00:00:00

  • Arabidopsis cryptochrome 2 (CRY2) functions by the photoactivation mechanism distinct from the tryptophan (trp) triad-dependent photoreduction.

    abstract::Cryptochromes are blue-light receptors mediating various light responses in plants and animals. The photochemical mechanism of cryptochromes is not well understood. It has been proposed that photoactivation of cryptochromes involves the blue-light-dependent photoreduction of flavin adenine dinucleotide via the electro...

    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.1114579108

    authors: Li X,Wang Q,Yu X,Liu H,Yang H,Zhao C,Liu X,Tan C,Klejnot J,Zhong D,Lin C

    更新日期:2011-12-20 00:00:00

  • Synthesis of mannosylglucosaminylinositol phospholipids in normal but not paroxysmal nocturnal hemoglobinuria cells.

    abstract::To identify mannosyl (Man)-containing intermediates of the human glycoinositol phospholipid (GPI) anchor pathway and examine their expression in paroxysmal nocturnal hemoglobinuria (PNH), mannolipid products deriving from in vitro guanosine diphosphate [3H]Man labeling of HeLa cell microsomes were characterized. The d...

    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.89.13.6025

    authors: Hirose S,Ravi L,Prince GM,Rosenfeld MG,Silber R,Andresen SW,Hazra SV,Medof ME

    更新日期:1992-07-01 00:00:00

  • Functional relevance of the histone gammaH2Ax in the response to DNA damaging agents.

    abstract::The phosphorylation of H2Ax on its S139 site, γH2Ax, is important during DNA double-strand repair and is considered necessary for assembly of repair complexes, but its functional role after other kinds of DNA damage is less clear. We have measured the survival of isogenic mouse cell lines with the H2Ax gene knocked ou...

    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.1105866108

    authors: Revet I,Feeney L,Bruguera S,Wilson W,Dong TK,Oh DH,Dankort D,Cleaver JE

    更新日期:2011-05-24 00:00:00

  • Expression of tandem gene duplicates is often greater than twofold.

    abstract::Tandem gene duplication is an important mutational process in evolutionary adaptation and human disease. Hypothetically, two tandem gene copies should produce twice the output of a single gene, but this expectation has not been rigorously investigated. Here, we show that tandem duplication often results in more than d...

    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.1605886113

    authors: Loehlin DW,Carroll SB

    更新日期:2016-05-24 00:00:00

  • X-ray structure of glutathione S-transferase from the malarial parasite Plasmodium falciparum.

    abstract::GSTs catalyze the conjugation of glutathione with a wide variety of hydrophobic compounds, generally resulting in nontoxic products that can be readily eliminated. In contrast to many other organisms, the malarial parasite Plasmodium falciparum possesses only one GST isoenzyme (PfGST). This GST is highly abundant in 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.2333763100

    authors: Fritz-Wolf K,Becker A,Rahlfs S,Harwaldt P,Schirmer RH,Kabsch W,Becker K

    更新日期:2003-11-25 00:00:00

  • Measuring the forces involved in polyvalent adhesion of uropathogenic Escherichia coli to mannose-presenting surfaces.

    abstract::Mechanisms of bacterial pathogenesis have become an increasingly important subject as pathogens have become increasingly resistant to current antibiotics. The adhesion of microorganisms to the surface of host tissue is often a first step in pathogenesis and is a plausible target for new antiinfective agents. Examinati...

    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.230451697

    authors: Liang MN,Smith SP,Metallo SJ,Choi IS,Prentiss M,Whitesides GM

    更新日期:2000-11-21 00:00:00

  • Purified, modified eel sodium channels are active in planar bilayers in the absence of activating neurotoxins.

    abstract::A recent study showed that limited trypsin treatment of liposomes containing purified Electrophorus electricus sodium channels activates a sodium radiotracer flux. We now report that similarly treated sodium channels show voltage-gated, tetrodotoxin-sensitive and highly sodium-selective single-channel currents when in...

    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.86.23.9592

    authors: Shenkel S,Cooper EC,James W,Agnew WS,Sigworth FJ

    更新日期:1989-12-01 00:00:00

  • The 3 × 120° rotary mechanism of Paracoccus denitrificans F1-ATPase is different from that of the bacterial and mitochondrial F1-ATPases.

    abstract::The rotation of Paracoccus denitrificans F1-ATPase (PdF1) was studied using single-molecule microscopy. At all concentrations of adenosine triphosphate (ATP) or a slowly hydrolyzable ATP analog (ATPγS), above or below Km, PdF1 showed three dwells per turn, each separated by 120°. Analysis of dwell time between steps 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.2003163117

    authors: Zarco-Zavala M,Watanabe R,McMillan DGG,Suzuki T,Ueno H,Mendoza-Hoffmann F,García-Trejo JJ,Noji H

    更新日期:2020-11-24 00:00:00

  • Cholesterol increases kinetic, energetic, and mechanical stability of the human β2-adrenergic receptor.

    abstract::The steroid cholesterol is an essential component of eukaryotic membranes, and it functionally modulates membrane proteins, including G protein-coupled receptors. To reveal insight into how cholesterol modulates G protein-coupled receptors, we have used dynamic single-molecule force spectroscopy to quantify the mechan...

    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.1210373109

    authors: Zocher M,Zhang C,Rasmussen SG,Kobilka BK,Müller DJ

    更新日期:2012-12-11 00:00:00

  • Antibodies to CD44 and integrin alpha4, but not L-selectin, prevent central nervous system inflammation and experimental encephalomyelitis by blocking secondary leukocyte recruitment.

    abstract::The role of various adhesion molecules in lymphocyte homing to the brain and in inflammatory autoimmune disease of the central nervous system (CNS) was examined in mice. Activated T cell lines and clones expressed CD44 and integrin alpha4, but not L-selectin, and entered the CNS independent of their antigen specificit...

    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.96.12.6896

    authors: Brocke S,Piercy C,Steinman L,Weissman IL,Veromaa T

    更新日期:1999-06-08 00:00:00

  • Constitutively high dNTP concentration inhibits cell cycle progression and the DNA damage checkpoint in yeast Saccharomyces cerevisiae.

    abstract::In eukaryotic cells the concentration of dNTP is highest in S phase and lowest in G1 phase and is controlled by ribonucleotide reductase (RNR). RNR activity is eliminated in all eukaryotes in G1 phase by a variety of mechanisms: transcriptional regulation, small inhibitory proteins, and protein degradation. After acti...

    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.0610585104

    authors: Chabes A,Stillman B

    更新日期:2007-01-23 00:00:00

  • In vitro selection of optimal DNA substrates for T4 RNA ligase.

    abstract::We have used in vitro selection techniques to characterize DNA sequences that are ligated efficiently by T4 RNA ligase. We find that the ensemble of selected sequences ligated about 10 times as efficiently as the random mixture of sequences used as the input for selection. Surprisingly, the majority of the selected se...

    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.90.4.1576

    authors: Harada K,Orgel LE

    更新日期:1993-02-15 00:00:00

  • The case for an ancestral genetic system involving simple analogues of the nucleotides.

    abstract::The idea that the first living systems on earth were based on self-replicating RNA molecules has recently become popular as a result of the discovery of ribozymes. However, there are several major problems associated with the prebiotic synthesis of ribonucleotides. In addition, there is the newly recognized problem of...

    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.84.13.4398

    authors: Joyce GF,Schwartz AW,Miller SL,Orgel LE

    更新日期:1987-07-01 00:00:00

  • Drosophila TFIIE: purification, cloning, and functional reconstitution.

    abstract::We present a physical and molecular genetic characterization of Drosophila melanogaster TFIIE (dTFIIE), a component of the basal RNA polymerase II transcription apparatus. We have purified dTFIIE to near homogeneity from nuclear extracts of Drosophila embryos and found that it is composed of two subunits with apparent...

    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.94.2.433

    authors: Wang X,Hansen SK,Ratts R,Zhou S,Snook AJ,Zehring W

    更新日期:1997-01-21 00:00:00

  • Channels formed by botulinum, tetanus, and diphtheria toxins in planar lipid bilayers: relevance to translocation of proteins across membranes.

    abstract::The heavy chains of both botulinum neurotoxin type B and tetanus toxin form channels in planar bilayer membranes. These channels have pH-dependent and voltage-dependent properties that are remarkably similar to those previously described for diphtheria toxin. Selectivity experiments with anions and cations show that 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.82.6.1692

    authors: Hoch DH,Romero-Mira M,Ehrlich BE,Finkelstein A,DasGupta BR,Simpson LL

    更新日期:1985-03-01 00:00:00

  • A soluble, high-affinity, interleukin-4-binding protein is present in the biological fluids of mice.

    abstract::Cytokines such as interleukin 4 (IL-4) play a key role in the regulation of immune responses, but little is known about how their multiple activities are regulated in vivo. In this report, we demonstrated that an IL-4-binding protein (IL-4BP) is constitutively present in the biological fluids of mice (serum, ascites, ...

    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.87.11.4202

    authors: Fernandez-Botran R,Vitetta ES

    更新日期:1990-06-01 00:00:00

  • A proposed function for spermine and spermidine: protection of replicating DNA against damage by singlet oxygen.

    abstract::Like all aliphatic amines, the polyamines spermine and spermidine are physical quenchers of singlet molecular oxygen (1O2*). The rate constants of these processes were determined in vitro with photochemically generated 1O2* and the hydrocarbon rubrene as substrate, in pyridine. At millimolar concentration, spermine 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.89.23.11426

    authors: Khan AU,Mei YH,Wilson T

    更新日期:1992-12-01 00:00:00