当前位置： SCI文献检索 > PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA期刊下所有文献 > GC/AT-content spikes as genomic punctuation marks.

GC/AT-content spikes as genomic punctuation marks.

Abstract：

:Large-scale analysis of the GC-content distribution at the gene level reveals both common features and basic differences in genomes of different groups of species. Sharp changes in GC content are detected at the transcription boundaries for all species analyzed, including human, mouse, rat, chicken, fruit fly, and worm. However, two substantially distinct groups of GC-content profiles can be recognized: warm-blooded vertebrates including human, mouse, rat, and chicken, and invertebrates including fruit fly and worm. In vertebrates, sharp positive and negative spikes of GC content are observed at the transcription start and stop sites, respectively, and there is also a progressive decrease in GC content from the 5' untranslated region to the 3' untranslated region along the gene. In invertebrates, the positive and negative GC-content spikes at the transcription start and stop sites are preceded by spikes of opposite value, and the highest GC content is found in the coding regions of the genes. Cross-correlation analysis indicates high frequencies of GC-content spikes at transcription start and stop sites. The strong conservation of this genomic feature seen in comparisons of the human/mouse and human/rat orthologs, and the clustering of genes with GC-content spikes on chromosomes imply a biological function. The GC-content spikes at transcription boundaries may reflect a general principle of genomic punctuation. Our analysis also provides means for identifying these GC-content spikes in individual genomic sequences.

journal_name

Proc Natl Acad Sci U S A

journal_title

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

authors

Zhang L,Kasif S,Cantor CR,Broude NE

doi

10.1073/pnas.0407821101

keywords:

subject

Has Abstract

pub_date

2004-11-30 00:00:00

pages

16855-60

issue

48

eissn

0027-8424

issn

1091-6490

pii

0407821101

journal_volume

101

pub_type

杂志文章

相关文献

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA文献大全
  • Long-term change in the organization of inventive activity.

    abstract：:Relying on a quantitative analysis of the patenting and assignment behavior of inventors, we highlight the evolution of institutions that encouraged trade in technology and a growing division of labor between those who invented new technologies and those who exploited them commercially over the nineteenth and early-tw...

    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.93.23.12686

    authors： Lamoreaux NR,Sokoloff KL

    更新日期：1996-11-12 00:00:00

  • A haplotype of the human CXCR1 gene protective against rapid disease progression in HIV-1+ patients.

    abstract：:Chemokines and their receptors are key factors in the onset and progression of AIDS. Among them, accumulating evidence strongly indicates the involvement of IL-8 and its receptors, CXCR1 and CXCR2, in AIDS-related conditions. Through extensive investigation of genetic variations of the human CXCR1-CXCR2 locus, we iden...

    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.0611670104

    authors： Vasilescu A,Terashima Y,Enomoto M,Heath S,Poonpiriya V,Gatanaga H,Do H,Diop G,Hirtzig T,Auewarakul P,Lauhakirti D,Sura T,Charneau P,Marullo S,Therwath A,Oka S,Kanegasaki S,Lathrop M,Matsushima K,Zagury JF,Matsuda

    更新日期：2007-02-27 00:00:00

  • Brain renin-angiotensin system blockade by systemically active aminopeptidase A inhibitors: a potential treatment of salt-dependent hypertension.

    abstract：:The hyperactivity of the brain renin-angiotensin system (RAS) has been implicated in the development and maintenance of hypertension in several types of experimental and genetic hypertension animal models. We previously reported that in the murine brain, aminopeptidase A (APA) is involved in the conversion of angioten...

    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.0402312101

    authors： Fournie-Zaluski MC,Fassot C,Valentin B,Djordjijevic D,Reaux-Le Goazigo A,Corvol P,Roques BP,Llorens-Cortes C

    更新日期：2004-05-18 00:00:00

  • Lysosomal storage disease upon disruption of the neuronal chloride transport protein ClC-6.

    abstract：:Mammalian CLC proteins function as Cl(-) channels or as electrogenic Cl(-)/H(+) exchangers and are present in the plasma membrane and intracellular vesicles. We now show that the ClC-6 protein is almost exclusively expressed in neurons of the central and peripheral nervous systems, with a particularly high expression ...

    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.0606137103

    authors： Poët M,Kornak U,Schweizer M,Zdebik AA,Scheel O,Hoelter S,Wurst W,Schmitt A,Fuhrmann JC,Planells-Cases R,Mole SE,Hübner CA,Jentsch TJ

    更新日期：2006-09-12 00:00:00

  • Complete nucleotide sequence of the gene for the specific glycoprotein (gp55) of Friend spleen focus-forming virus.

    abstract：:The complete nucleotide sequence of the gene for the specific glycoprotein (gp55) of the polycythemic strain of Friend spleen focus-forming virus (SFFV) was derived from the cloned SFFV DNA intermediate. The gp55 gene is present within 1.4 kilobases of the 5' side of the 3'long terminal repeat sequence. The open readi...

    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.80.13.3913

    authors： Amanuma H,Katori A,Obata M,Sagata N,Ikawa Y

    更新日期：1983-07-01 00:00:00

  • Controllability in protein interaction networks.

    abstract：:Recently, the focus of network research shifted to network controllability, prompting us to determine proteins that are important for the control of the underlying interaction webs. In particular, we determined minimum dominating sets of proteins (MDSets) in human and yeast protein interaction networks. Such groups 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.1311231111

    authors： Wuchty S

    更新日期：2014-05-13 00:00:00

  • Fermentation of dihydroxyacetone by engineered Escherichia coli and Klebsiella variicola to products.

    abstract：:Methane can be converted to triose dihydroxyacetone (DHA) by chemical processes with formaldehyde as an intermediate. Carbon dioxide, a by-product of various industries including ethanol/butanol biorefineries, can also be converted to formaldehyde and then to DHA. DHA, upon entry into a cell and phosphorylation to DHA...

    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.1801002115

    authors： Wang L,Chauliac D,Rhee MS,Panneerselvam A,Ingram LO,Shanmugam KT

    更新日期：2018-04-24 00:00:00

  • Defective human interleukin 2 receptor gamma chain in an atypical X chromosome-linked severe combined immunodeficiency with peripheral T cells.

    abstract：:X chromosome-linked severe combined immunodeficiency disease (SCIDX1) is characterized by the absence of T-cell and natural killer cell development and results from molecular mutations of the interleukin 2 receptor (IL-2R) gamma chain. The IL-2R gamma chain is a common component of the IL-2, IL-4, and IL-7 receptor sy...

    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.91.20.9466

    authors： DiSanto JP,Rieux-Laucat F,Dautry-Varsat A,Fischer A,de Saint Basile G

    更新日期：1994-09-27 00:00:00

  • Trimodal low-dose X-ray tomography.

    abstract：:X-ray grating interferometry is a coherent imaging technique that bears tremendous potential for three-dimensional tomographic imaging of soft biological tissue and other specimens whose details exhibit very weak absorption contrast. It is intrinsically trimodal, delivering phase contrast, absorption contrast, and sca...

    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.1117861109

    authors： Zanette I,Bech M,Rack A,Le Duc G,Tafforeau P,David C,Mohr J,Pfeiffer F,Weitkamp T

    更新日期：2012-06-26 00:00:00

  • Selectivity at the cleavage/attachment site of phosphatidylinositol-glycan anchored membrane proteins is enzymatically determined.

    abstract：:Nascent precursors of phosphatidylinositol-glycan (PI-G)-linked membrane proteins contain a hydrophobic COOH-terminal sequence of 15-30 residues that is eliminated during processing to yield a newly exposed COOH terminus to which the PI-G moiety is added. There is no consensus as to the primary structure of the termin...

    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.87.20.7939

    authors： Micanovic R,Kodukula K,Gerber LD,Udenfriend S

    更新日期：1990-10-01 00:00:00

  • Human acetyl-CoA carboxylase 1 gene: presence of three promoters and heterogeneity at the 5'-untranslated mRNA region.

    abstract：:Acetyl-CoA carboxylase 1 (ACC1) catalyzes the formation of malonyl-CoA, the C2 donor for de novo synthesis of long-chain fatty acids. We have identified 64 exons, including 7 alternatively spliced minor exons (1A, 1B, 1C, 3, 5A', 5A, and 5B) in human ACC1 gene ( approximately 330 kb). The gene is regulated by three pr...

    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.1332670100

    authors： Mao J,Chirala SS,Wakil SJ

    更新日期：2003-06-24 00:00:00

  • Microbiota promotes systemic T-cell survival through suppression of an apoptotic factor.

    abstract：:Symbiotic microbes impact the severity of a variety of diseases through regulation of T-cell development. However, little is known regarding the molecular mechanisms by which this is accomplished. Here we report that a secreted factor, Erdr1, is regulated by the microbiota to control T-cell apoptosis. Erdr1 expression...

    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.1619336114

    authors： Soto R,Petersen C,Novis CL,Kubinak JL,Bell R,Stephens WZ,Lane TE,Fujinami RS,Bosque A,O'Connell RM,Round JL

    更新日期：2017-05-23 00:00:00

  • Mosaic organization and heterogeneity in frequency of allelic recombination of the Plasmodium vivax merozoite surface protein-1 locus.

    abstract：:The organization and allelic recombination of the merozoite surface protein-1 gene of Plasmodium vivax (PvMsp-1), the most widely prevalent human malaria parasite, were evaluated in complete nucleotide sequences of 40 isolates from various geographic areas. Alignment of 31 distinct alleles revealed the mosaic organiza...

    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.252348999

    authors： Putaporntip C,Jongwutiwes S,Sakihama N,Ferreira MU,Kho WG,Kaneko A,Kanbara H,Hattori T,Tanabe K

    更新日期：2002-12-10 00:00:00

  • Overexpression of Cu-Zn superoxide dismutase in Drosophila does not affect life-span.

    abstract：:Aging and disease processes may be due to deleterious and irreversible changes produced by free radical reactions. The enzyme copper-zinc superoxide dismutase (Cu-Zn SOD; superoxide:superoxide oxidoreductase, EC 1.15.1.1) performs a protective function by scavenging superoxide radicals. The Cu-Zn SOD gene (Sod) cloned...

    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.87.11.4270

    authors： Seto NO,Hayashi S,Tener GM

    更新日期：1990-06-01 00:00:00

  • Mutations in the bglY gene increase the frequency of spontaneous deletions in Escherichia coli K-12.

    abstract：:A strong mutator effect has been observed in Escherichia coli K-12 strains mutated in the bglY gene (27 min). The frequency of point mutations is not modified in bglY mutant strains. In contrast, a strong increase in spontaneous generation of large deletions has been observed in these strains, both for chromosomal mar...

    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.87.1.360

    authors： Lejeune P,Danchin A

    更新日期：1990-01-01 00:00:00

  • Preparation of a disulfide-linked dimer of human placental lactogen fragment 1--134 with immunologic and biologic activity.

    abstract：:In order to determine the chemical features of human placental lactogen (hPL) necessary for its biologic activity we prepared the following fragments from the plasmin-cleaved hormone: reduced and alkylated 1--134, reduced and alkylated 141--191, and a 1--134 dimer joined through the single cysteinyl residue at positio...

    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.76.3.1204

    authors： Russell J,Sherwood LM,Kowalski K,Schneider AB

    更新日期：1979-03-01 00:00:00

  • A nonparametric view of network models and Newman-Girvan and other modularities.

    abstract：:Prompted by the increasing interest in networks in many fields, we present an attempt at unifying points of view and analyses of these objects coming from the social sciences, statistics, probability and physics communities. We apply our approach to the Newman-Girvan modularity, widely used for "community" detection, ...

    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.0907096106

    authors： Bickel PJ,Chen A

    更新日期：2009-12-15 00:00:00

  • Free entropy and property T factors.

    abstract：:We show that a large class of finite factors has free entropy dimension less than or equal to one. This class includes all prime factors and many property T factors. ...

    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.97.18.9881

    authors： Ge L,Shen J

    更新日期：2000-08-29 00:00:00

  • A gene required for transfer of T-DNA to plants encodes an ATPase with autophosphorylating activity.

    abstract：:The virB operon of the Agrobacterium tume-faciens pTiA6NC plasmid likely plays a role in directing T-DNA transfer events at the bacterial membrane, as determined previously by mutagenesis and cellular fractionation studies and by DNA sequence analysis of the approximately 12-kilobase-pair operon. The DNA sequence anal...

    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.86.24.9677

    authors： Christie PJ,Ward JE Jr,Gordon MP,Nester EW

    更新日期：1989-12-01 00:00:00

  • An early role for sonic hedgehog from foregut endoderm in jaw development: ensuring neural crest cell survival.

    abstract：:We have investigated the role of Sonic hedgehog (Shh) in the development of facial structures by depriving chicken embryos of the most anterior sources of this morphogen, including the prechordal plate and the anterior ventral endoderm of the foregut, before the onset of neural crest cell (NCC) migration to the first ...

    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.0604751103

    authors： Brito JM,Teillet MA,Le Douarin NM

    更新日期：2006-08-01 00:00:00

  • Neuroglobin attenuates beta-amyloid neurotoxicity in vitro and transgenic Alzheimer phenotype in vivo.

    abstract：:Neuroglobin (Ngb), a vertebrate globin expressed primarily in neurons, is induced by and protects against neuronal hypoxia and cerebral ischemia. To investigate the spectrum and mechanism of Ngb's neuroprotective action, we studied the effect of transgenic overexpression of Ngb on NMDA and beta-amyloid (Abeta) toxicit...

    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.0706167104

    authors： Khan AA,Mao XO,Banwait S,Jin K,Greenberg DA

    更新日期：2007-11-27 00:00:00

  • Galanin inhibits acetylcholine release in the ventral hippocampus of the rat: histochemical, autoradiographic, in vivo, and in vitro studies.

    abstract：:A high density of galanin binding sites was found by using 125I-labeled galanin, iodinated by chloramine-T, followed by autoradiography in the ventral, but not in the dorsal, hippocampus of the rat. Lesions of the fimbria and of the septum caused disappearance of a major population of these binding sites, suggesting 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.84.20.7339

    authors： Fisone G,Wu CF,Consolo S,Nordström O,Brynne N,Bartfai T,Melander T,Hökfelt T

    更新日期：1987-10-01 00:00:00

  • In situ growth of a PEG-like polymer from the C terminus of an intein fusion protein improves pharmacokinetics and tumor accumulation.

    abstract：:This paper reports a general in situ method to grow a polymer conjugate solely from the C terminus of a recombinant protein. GFP was fused at its C terminus with an intein; cleavage of the intein provided a unique thioester moiety at the C terminus of GFP that was used to install an atom transfer radical polymerizatio...

    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.1006044107

    authors： Gao W,Liu W,Christensen T,Zalutsky MR,Chilkoti A

    更新日期：2010-09-21 00:00:00

  • Signal peptide-chaperone interactions on the twin-arginine protein transport pathway.

    abstract：:The twin-arginine transport (Tat) system is a protein-targeting pathway of prokaryotes and chloroplasts. Most Escherichia coli Tat substrates are complex metalloenzymes that must be correctly folded and assembled before transport, and a preexport chaperone-mediated "proofreading" process is therefore in operation. The...

    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.0500737102

    authors： Hatzixanthis K,Clarke TA,Oubrie A,Richardson DJ,Turner RJ,Sargent F

    更新日期：2005-06-14 00:00:00

  • ABCA7 haplodeficiency disturbs microglial immune responses in the mouse brain.

    abstract：:Carrying premature termination codons in 1 allele of the ABCA7 gene is associated with an increased risk for Alzheimer's disease (AD). While the primary function of ABCA7 is to regulate the transport of phospholipids and cholesterol, ABCA7 is also involved in maintaining homeostasis of the immune system. Since inflamm...

    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.1908529116

    authors： Aikawa T,Ren Y,Yamazaki Y,Tachibana M,Johnson MR,Anderson CT,Martens YA,Holm ML,Asmann YW,Saito T,Saido TC,Fitzgerald ML,Bu G,Kanekiyo T

    更新日期：2019-11-19 00:00:00

  • Expression and crystallization of the complex of HLA-DR2 (DRA, DRB1*1501) and an immunodominant peptide of human myelin basic protein.

    abstract：:HLA-DR2 is associated with susceptibility to multiple sclerosis (MS). A peptide from human myelin basic protein (MBP, residues 85-99) was previously found to bind to purified HLA-DR2 (DRA, DRB1*1501) and to be recognized by human MBP-specific T cell clones. Soluble HLA-DR2 was expressed in the baculovirus system by re...

    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.95.20.11828

    authors： Gauthier L,Smith KJ,Pyrdol J,Kalandadze A,Strominger JL,Wiley DC,Wucherpfennig KW

    更新日期：1998-09-29 00:00:00

  • Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein.

    abstract：:Many bacteria use acyl homoserine lactone signals to monitor cell density in a type of gene regulation termed quorum sensing and response. Synthesis of these signals is directed by homologs of the luxi gene of Vibrio fischeri. This communication resolves two critical issues concerning the synthesis of the V. fischeri ...

    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.93.18.9505

    authors： Schaefer AL,Val DL,Hanzelka BL,Cronan JE Jr,Greenberg EP

    更新日期：1996-09-03 00:00:00

  • Thiazide diuretic drug receptors in rat kidney: identification with [3H]metolazone.

    abstract：:Thiazides and related diuretics inhibit NaCl reabsorption in the distal tubule through an unknown mechanism. We report here that [3H]metolazone, a diuretic with a thiazide-like mechanism of action, labels a site in rat kidney membranes that has characteristics of the thiazide-sensitive ion transporter. [3H]Metolazone ...

    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.85.7.2311

    authors： Beaumont K,Vaughn DA,Fanestil DD

    更新日期：1988-04-01 00:00:00

  • Rat cardiac ventricle has two Na+,K+-ATPases with different affinities for ouabain: developmental changes in immunologically different catalytic subunits.

    abstract：:The mechanism of the inotropic effect of cardiac glycosides on the heart has long been controversial. Inotropic effects at low concentrations of cardiac glycosides indicate more than one class of receptor or more than one cellular mechanism. In the brain of the rat, high- and low-affinity cardiac glycoside receptors h...

    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.84.23.8404

    authors： Sweadner KJ,Farshi SK

    更新日期：1987-12-01 00:00:00

  • Spectrum of hot methane in astronomical objects using a comprehensive computed line list.

    abstract：:Hot methane spectra are important in environments ranging from flames to the atmospheres of cool stars and exoplanets. A new spectroscopic line list, 10to10, for (12)CH4 containing almost 10 billion transitions is presented. This comprehensive line list covers a broad spectroscopic range and is applicable for temperat...

    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.1324219111

    authors： Yurchenko SN,Tennyson J,Bailey J,Hollis MD,Tinetti G

    更新日期：2014-07-01 00:00:00