当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > Codon catalog usage and the genome hypothesis.

Codon catalog usage and the genome hypothesis.

Abstract：

:Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind of genome, appears to possess a "system" for choosing between codons. Frameshift genes, however, have widely different choice strategies from normal genes. Our work indicates that the main factors distinguishing between mRNA sequences relate to choices among degenerate bases. These systematic third base choices can therefore be used to establish a new kind of genetic distance, which reflects differences in coding strategy. The choice patterns we find seem compatible with the idea that the genome and not the individual gene is the unit of selection. Each gene in a genome tends to conform to its species' usage of the codon catalog; this is our genome hypothesis.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Grantham R,Gautier C,Gouy M,Mercier R,Pavé A

doi

10.1093/nar/8.1.197-c

subject

Has Abstract

pub_date

1980-01-11 00:00:00

pages

r49-r62

issue

1

eissn

0305-1048

issn

1362-4962

journal_volume

8

pub_type

杂志文章,评审

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • Sequence-dependent off-target inhibition of TLR7/8 sensing by synthetic microRNA inhibitors.

    abstract：:Anti-microRNA (miRNA) oligonucleotides (AMOs) with 2'-O-Methyl (2'OMe) residues are commonly used to study miRNA function and can achieve high potency, with low cytotoxicity. Not withstanding this, we demonstrate the sequence-dependent capacity of 2'OMe AMOs to inhibit Toll-like receptor (TLR) 7 and 8 sensing of immun...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku1343

    authors： Sarvestani ST,Stunden HJ,Behlke MA,Forster SC,McCoy CE,Tate MD,Ferrand J,Lennox KA,Latz E,Williams BR,Gantier MP

    更新日期：2015-01-01 00:00:00

  • Sequences of three promoters for the bacteriophage SP6 RNA polymerase.

    abstract：:Fragments of SP6 DNA generated by cleavage with Hpa II or Taq I were cloned into the Cla I site of pBR322 and the recombinant plasmids were screened for the presence of SP6 promoter activity by transcription in vitro with purified SP6 RNA polymerase. Three plasmids having promoter activity and small inserts of SP6 DNA...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/14.8.3521

    authors： Brown JE,Klement JF,McAllister WT

    更新日期：1986-04-25 00:00:00

  • Ku heterodimer binds to both ends of the Werner protein and functional interaction occurs at the Werner N-terminus.

    abstract：:The human Werner syndrome protein, WRN, is a member of the RecQ helicase family and contains 3'-->5' helicase and 3'-->5' exonuclease activities. Recently, we showed that the exonuclease activity of WRN is greatly stimulated by the human Ku heterodimer protein. We have now mapped this interaction physically and functi...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkf482

    authors： Karmakar P,Snowden CM,Ramsden DA,Bohr VA

    更新日期：2002-08-15 00:00:00

  • Differential roles for Fos and Jun in DNA-binding: redox-dependent and independent functions.

    abstract：:The Fos and Jun family of transcription factors contain an invariant sequence motif lysine-cysteine-arginine (KCR) in the highly conserved DNA-binding region. Reduction of the cysteine residue is necessary to facilitate DNA-binding. Here, we examined the potential dual roles of the flanking lysine and arginine residue...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/21.25.5831

    authors： Ng L,Forrest D,Curran T

    更新日期：1993-12-25 00:00:00

  • An electrophoretic karyotype for Schizosaccharomyces pombe by pulsed field gel electrophoresis.

    abstract：:The three chromosomal DNAs of S. pombe have been fractionated by pulsed field gel electrophoresis. The resulting molecular karyotype will greatly speed gene mapping in this organism, and it indicates that the separation range of the technique extends to DNA molecules as large as 9,000,000 base pairs. ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/15.11.4481

    authors： Smith CL,Matsumoto T,Niwa O,Klco S,Fan JB,Yanagida M,Cantor CR

    更新日期：1987-06-11 00:00:00

  • Identification of HDA15-PIF1 as a key repression module directing the transcriptional network of seed germination in the dark.

    abstract：:Light is a major external factor in regulating seed germination. Photoreceptor phytochrome B (PHYB) plays a predominant role in promoting seed germination in the initial phase after imbibition, partially by repressing phytochrome-interacting factor1 (PIF1). However, the mechanism underlying the PHYB-PIF1-mediated tran...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx283

    authors： Gu D,Chen CY,Zhao M,Zhao L,Duan X,Duan J,Wu K,Liu X

    更新日期：2017-07-07 00:00:00

  • Kinetic studies on the formation of intermolecular triple helices.

    abstract：:We have used DNase I footprinting to examine the association kinetics of GA-, GT- and CT-containing oligonucleotides with the target sequence (GGA)5GG. (CCT)5CC. These reactions are slow yielding bimolecular association rate constants between 50 and 2000 M-1s-1. We find that GT-containing oligonucleotides bind much fa...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/25.16.3269

    authors： Paes HM,Fox KR

    更新日期：1997-08-15 00:00:00

  • High efficiency error suppression for accurate detection of low-frequency variants.

    abstract：:Detection of cancer-associated somatic mutations has broad applications for oncology and precision medicine. However, this becomes challenging when cancer-derived DNA is in low abundance, such as in impure tissue specimens or in circulating cell-free DNA. Next-generation sequencing (NGS) is particularly prone to techn...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz474

    authors： Wang TT,Abelson S,Zou J,Li T,Zhao Z,Dick JE,Shlush LI,Pugh TJ,Bratman SV

    更新日期：2019-09-05 00:00:00

  • Coding capacity of complementary DNA strands.

    abstract：:A Fortran computer algorithm has been used to analyze the nucleotide sequence of several structural genes. The analysis performed on both coding and complementary DNA strands shows that whereas open reading frames shorter than 100 codons are randomly distributed on both DNA strands, open reading frames longer than 100...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/9.6.1499

    authors： Casino A,Cipollaro M,Guerrini AM,Mastrocinque G,Spena A,Scarlato V

    更新日期：1981-03-25 00:00:00

  • ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.

    abstract：:Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction data...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl783

    authors： Obayashi T,Kinoshita K,Nakai K,Shibaoka M,Hayashi S,Saeki M,Shibata D,Saito K,Ohta H

    更新日期：2007-01-01 00:00:00

  • Specific bonding of puromycin to full-length protein at the C-terminus.

    abstract：:Puromycin, an analog of the 3' end of aminoacyl-tRNA, causes premature termination of translation by being linked non-specifically to growing polypeptide chains. Here we report the interesting phenomenon that puromycin acting as a non-inhibitor at very low concentration (e.g. 0.04 microM) can bond only to full-length ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/28.5.1176

    authors： Miyamoto-Sato E,Nemoto N,Kobayashi K,Yanagawa H

    更新日期：2000-03-01 00:00:00

  • Nucleosome positioning as a critical determinant for the DNA cleavage sites of mammalian DNA topoisomerase II in reconstituted simian virus 40 chromatin.

    abstract：:We have assessed the ability of nucleosomes to influence the formation of mammalian topoisomerase II-DNA complexes by mapping the sites of cleavage induced by four unrelated topoisomerase II inhibitors in naked versus nucleosome-reconstituted SV40 DNA. DNA fragments were reconstituted with histone octamers from HeLa c...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/18.15.4553

    authors： Capranico G,Jaxel C,Roberge M,Kohn KW,Pommier Y

    更新日期：1990-08-11 00:00:00

  • Telomeric circles are abundant in the stn1-M1 mutant that maintains its telomeres through recombination.

    abstract：:Some human cancers maintain their telomeres using the alternative lengthening of telomeres (ALT) mechanism; a process thought to involve recombination. Different types of recombinational telomere elongation pathways have been identified in yeasts. In senescing yeast telomerase deletion (ter1-Delta) mutants with very s...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkp814

    authors： Basenko EY,Cesare AJ,Iyer S,Griffith JD,McEachern MJ

    更新日期：2010-01-01 00:00:00

  • PRP28, a 'DEAD-box' protein, is required for the first step of mRNA splicing in vitro.

    abstract：:We previously reported the isolation of PRP28, a gene in Saccharomyces cerevisiae whose activity is required for the first step of nuclear mRNA splicing in vivo. Sequence analysis revealed that PRP28 is included in the 'DEAD-box' gene family, members of which are thought to function as ATP-dependent RNA helicases. Gen...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/22.15.3187

    authors： Strauss EJ,Guthrie C

    更新日期：1994-08-11 00:00:00

  • A single-stranded DNA-binding protein shared by telomeric repeats, the variant surface glycoprotein transcription promoter and the procyclin transcription terminator of Trypanosoma brucei.

    abstract：:In Trypanosoma brucei the genes are organised into long polycistronic transcription units and only three promoters for protein-encoding genes and a single terminator have been characterised. These promoters recruit a polI-like RNA polymerase for the transcription units encoding the two major stage-specific antigens of...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/28.2.597

    authors： Berberof M,Vanhamme L,Alexandre S,Lips S,Tebabi P,Pays E

    更新日期：2000-01-15 00:00:00

  • Determinants of a transcriptionally competent environment at the GM-CSF promoter.

    abstract：:Granulocyte macrophage-colony stimulating factor (GM-CSF) is produced by T cells, but not B cells, in response to immune signals. GM-CSF gene activation in response to T-cell stimulation requires remodelling of chromatin associated with the gene promoter, and these changes do not occur in B cells. While the CpG methyl...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn117

    authors： Brettingham-Moore KH,Sprod OR,Chen X,Oakford P,Shannon MF,Holloway AF

    更新日期：2008-05-01 00:00:00

  • PhEVER: a database for the global exploration of virus-host evolutionary relationships.

    abstract：:Fast viral adaptation and the implication of this rapid evolution in the emergence of several new infectious diseases have turned this issue into a major challenge for various research domains. Indeed, viruses are involved in the development of a wide range of pathologies and understanding how viruses and host cells i...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1013

    authors： Palmeira L,Penel S,Lotteau V,Rabourdin-Combe C,Gautier C

    更新日期：2011-01-01 00:00:00

  • Human replication protein A can suppress the intrinsic in vitro mutator phenotype of human DNA polymerase lambda.

    abstract：:DNA polymerase lambda (pol lambda) is a member of the X family DNA polymerases and is endowed with multiple enzymatic activities. In this work we investigated the in vitro miscoding properties of full-length, human pol lambda either in the absence or in the presence of the human auxiliary proteins proliferating cell n...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl032

    authors： Maga G,Shevelev I,Villani G,Spadari S,Hübscher U

    更新日期：2006-03-06 00:00:00

  • Solid phase synthesis of oligoribonucleotides using the 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl (Ctmp) group for the protection of the 2'-hydroxy functions and the H-phosphonate approach.

    abstract：:The solid phase synthesis of oligoribonucleotides using the H-phosphonate approach and the 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl (Ctmp) and dimethoxytrityl (DMTr) groups, respectively, for the protection of the 2'- and 5'-hydroxy functions is described. The use of a new reagent, tris-(1,1,1,3,3,3-hexaf...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/17.10.3689

    authors： Sakatsume O,Ohtsuki M,Takaku H,Reese CB

    更新日期：1989-05-25 00:00:00

  • Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions.

    abstract：:Multicellular organismal development is controlled by a complex network of transcription factors, promoters and enhancers. Although reliable computational and experimental methods exist for enhancer detection, prediction of their target genes remains a major challenge. On the basis of available literature and ChIP-seq...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1081

    authors： Rödelsperger C,Guo G,Kolanczyk M,Pletschacher A,Köhler S,Bauer S,Schulz MH,Robinson PN

    更新日期：2011-04-01 00:00:00

  • Apple II software for M13 shotgun DNA sequencing.

    abstract：:A set of programs is presented for the reconstruction of a DNA sequence from data generated by the M13 shotgun sequencing technique. Once the sequence has been established and stored other programs are used for its analysis. The programs have been written for the Apple II microcomputer. A minimum investment is require...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/10.1.39

    authors： Larson R,Messing J

    更新日期：1982-01-11 00:00:00

  • A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control.

    abstract：:Tumor formation is partially driven by DNA copy number changes, which are typically measured using array comparative genomic hybridization, SNP arrays and DNA sequencing platforms. Many techniques are available for detecting recurring aberrations across multiple tumor samples, including CMAR, STAC, GISTIC and KC-SMART...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt155

    authors： van Dyk E,Reinders MJ,Wessels LF

    更新日期：2013-05-01 00:00:00

  • CAF-1-induced oligomerization of histones H3/H4 and mutually exclusive interactions with Asf1 guide H3/H4 transitions among histone chaperones and DNA.

    abstract：:Anti-silencing function 1 (Asf1) and Chromatin Assembly Factor 1 (CAF-1) chaperone histones H3/H4 during the assembly of nucleosomes on newly replicated DNA. To understand the mechanism of histone H3/H4 transfer among Asf1, CAF-1 and DNA from a thermodynamic perspective, we developed and employed biophysical approache...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks906

    authors： Liu WH,Roemer SC,Port AM,Churchill ME

    更新日期：2012-12-01 00:00:00

  • The Mouse Gene Expression Database (GXD).

    abstract：:The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling val...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.1.98

    authors： Ringwald M,Eppig JT,Begley DA,Corradi JP,McCright IJ,Hayamizu TF,Hill DP,Kadin JA,Richardson JE

    更新日期：2001-01-01 00:00:00

  • SUVH1, a Su(var)3-9 family member, promotes the expression of genes targeted by DNA methylation.

    abstract：:Transposable elements are found throughout the genomes of all organisms. Repressive marks such as DNA methylation and histone H3 lysine 9 (H3K9) methylation silence these elements and maintain genome integrity. However, how silencing mechanisms are themselves regulated to avoid the silencing of genes remains unclear. ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv958

    authors： Li S,Liu L,Li S,Gao L,Zhao Y,Kim YJ,Chen X

    更新日期：2016-01-29 00:00:00

  • Swc4 positively regulates telomere length independently of its roles in NuA4 and SWR1 complexes.

    abstract：:Telomeres at the ends of eukaryotic chromosomes are essential for genome integrality and stability. In order to identify genes that sustain telomere maintenance independently of telomerase recruitment, we have exploited the phenotype of over-long telomeres in the cells that express Cdc13-Est2 fusion protein, and exami...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkaa1150

    authors： Liu JC,Li QJ,He MH,Hu C,Dai P,Meng FL,Zhou BO,Zhou JQ

    更新日期：2020-12-16 00:00:00

  • A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells.

    abstract：:Integration of foreign genes into plant genomes by the Agrobacterium T-DNA transfer system has been considered to occur at random. It has been speculated that the chromosomal structure of the integration site might affect the expression pattern of the introduced genes. To gain insight into the molecular structure of T...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/22.14.2744

    authors： Dietz A,Kay V,Schlake T,Landsmann J,Bode J

    更新日期：1994-07-25 00:00:00

  • Biochemical properties of oligo [(+)-carbocyclic-thymidylates] and their complexes.

    abstract：:We report here spectroscopic and biochemical data of a novel series of sugar-modified oligodeoxy-nucleotides, the carbocyclic oligothymidylates, c(dT)3-20. In c(dT)n a methylene group has been substituted for the oxygen atom of the deoxyribose ring of the natural thymidylate unit. c(dT)10-20 form helical structures, i...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/18.8.2133

    authors： Sági J,Szemzõ A,Szécsi J,Otvös L

    更新日期：1990-04-25 00:00:00

  • Allegro: analyzing expression and sequence in concert to discover regulatory programs.

    abstract：:A major goal of system biology is the characterization of transcription factors and microRNAs (miRNAs) and the transcriptional programs they regulate. We present Allegro, a method for de-novo discovery of cis-regulatory transcriptional programs through joint analysis of genome-wide expression data and promoter or 3' U...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn1064

    authors： Halperin Y,Linhart C,Ulitsky I,Shamir R

    更新日期：2009-04-01 00:00:00

  • Sequence-specific DNA recognition by the thyroid transcription factor-1 homeodomain.

    abstract：:The molecular basis for the DNA binding specificity of the thyroid transcription factor 1 homeodomain (TTF-1HD) has been investigated. Methylation and ethylation interference experiments show that the TTF-1HD alone recapitulates the DNA binding properties of the entire protein. Studies carried out with mutant derivati...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/22.15.3075

    authors： Damante G,Fabbro D,Pellizzari L,Civitareale D,Guazzi S,Polycarpou-Schwartz M,Cauci S,Quadrifoglio F,Formisano S,Di Lauro R

    更新日期：1994-08-11 00:00:00