Literature DB >> 11282969

Genome-scale compositional comparisons in eukaryotes.

A J Gentles1, S Karlin.   

Abstract

We examined dinucleotide relative abundances and their biases in recent sequences of eukaryotic genomes and chromosomes, including human chromosomes 21 and 22, Saccharomyces cerevisiae, Arabidopsis thaliana, and Drosophila melanogaster. We found that dinucleotide relative abundances are remarkably constant across human chromosomes and within the DNA of a particular species. The dinucleotide biases differ between species, providing a genome signature that is characteristic of the bulk properties of an organism's DNA. We detail the relations between species genome signatures and suggest possible mechanisms for their origin and maintenance.

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Year:  2001        PMID： 11282969      PMCID： PMC311039          DOI： 10.1101/gr.163101

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  22 in total

1.  The DNA sequence of human chromosome 21.

Authors:  M Hattori; A Fujiyama; T D Taylor; H Watanabe; T Yada; H S Park; A Toyoda; K Ishii; Y Totoki; D K Choi; Y Groner; E Soeda; M Ohki; T Takagi; Y Sakaki; S Taudien; K Blechschmidt; A Polley; U Menzel; J Delabar; K Kumpf; R Lehmann; D Patterson; K Reichwald; A Rump; M Schillhabel; A Schudy; W Zimmermann; A Rosenthal; J Kudoh; K Schibuya; K Kawasaki; S Asakawa; A Shintani; T Sasaki; K Nagamine; S Mitsuyama; S E Antonarakis; S Minoshima; N Shimizu; G Nordsiek; K Hornischer; P Brant; M Scharfe; O Schon; A Desario; J Reichelt; G Kauer; H Blocker; J Ramser; A Beck; S Klages; S Hennig; L Riesselmann; E Dagand; T Haaf; S Wehrmeyer; K Borzym; K Gardiner; D Nizetic; F Francis; H Lehrach; R Reinhardt; M L Yaspo
Journal:  Nature       Date:  2000-05-18       Impact factor: 49.962

2.  Doublet frequency analysis of fractionated vertebrate nuclear DNA.

Authors:  G J Russell; P M Walker; R A Elton; J H Subak-Sharpe
Journal:  J Mol Biol       Date:  1976-11       Impact factor: 5.469

Review 3.  Biological asymmetries and the fidelity of eukaryotic DNA replication.

Authors:  T A Kunkel
Journal:  Bioessays       Date:  1992-05       Impact factor: 4.345

Review 4.  Fidelity mechanisms in DNA replication.

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Journal:  Annu Rev Biochem       Date:  1991       Impact factor: 23.643

5.  Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage.

Authors:  E Beutler; T Gelbart; J H Han; J A Koziol; B Beutler
Journal:  Proc Natl Acad Sci U S A       Date:  1989-01       Impact factor: 11.205

6.  Similarity of the general designs of protochordates and invertebrates.

Authors:  G J Russell; J H Subak-Sharpe
Journal:  Nature       Date:  1977-04-07       Impact factor: 49.962

7.  CC dinucleotides contribute to the bending of DNA in chromatin.

Authors:  A Bolshoy
Journal:  Nat Struct Biol       Date:  1995-06

8.  Comparisons of eukaryotic genomic sequences.

Authors:  S Karlin; I Ladunga
Journal:  Proc Natl Acad Sci U S A       Date:  1994-12-20       Impact factor: 11.205

9.  Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses?

Authors:  S Karlin; W Doerfler; L R Cardon
Journal:  J Virol       Date:  1994-05       Impact factor: 5.103

10.  The genome sequence of Drosophila melanogaster.

Authors:  M D Adams; S E Celniker; R A Holt; C A Evans; J D Gocayne; P G Amanatides; S E Scherer; P W Li; R A Hoskins; R F Galle; R A George; S E Lewis; S Richards; M Ashburner; S N Henderson; G G Sutton; J R Wortman; M D Yandell; Q Zhang; L X Chen; R C Brandon; Y H Rogers; R G Blazej; M Champe; B D Pfeiffer; K H Wan; C Doyle; E G Baxter; G Helt; C R Nelson; G L Gabor; J F Abril; A Agbayani; H J An; C Andrews-Pfannkoch; D Baldwin; R M Ballew; A Basu; J Baxendale; L Bayraktaroglu; E M Beasley; K Y Beeson; P V Benos; B P Berman; D Bhandari; S Bolshakov; D Borkova; M R Botchan; J Bouck; P Brokstein; P Brottier; K C Burtis; D A Busam; H Butler; E Cadieu; A Center; I Chandra; J M Cherry; S Cawley; C Dahlke; L B Davenport; P Davies; B de Pablos; A Delcher; Z Deng; A D Mays; I Dew; S M Dietz; K Dodson; L E Doup; M Downes; S Dugan-Rocha; B C Dunkov; P Dunn; K J Durbin; C C Evangelista; C Ferraz; S Ferriera; W Fleischmann; C Fosler; A E Gabrielian; N S Garg; W M Gelbart; K Glasser; A Glodek; F Gong; J H Gorrell; Z Gu; P Guan; M Harris; N L Harris; D Harvey; T J Heiman; J R Hernandez; J Houck; D Hostin; K A Houston; T J Howland; M H Wei; C Ibegwam; M Jalali; F Kalush; G H Karpen; Z Ke; J A Kennison; K A Ketchum; B E Kimmel; C D Kodira; C Kraft; S Kravitz; D Kulp; Z Lai; P Lasko; Y Lei; A A Levitsky; J Li; Z Li; Y Liang; X Lin; X Liu; B Mattei; T C McIntosh; M P McLeod; D McPherson; G Merkulov; N V Milshina; C Mobarry; J Morris; A Moshrefi; S M Mount; M Moy; B Murphy; L Murphy; D M Muzny; D L Nelson; D R Nelson; K A Nelson; K Nixon; D R Nusskern; J M Pacleb; M Palazzolo; G S Pittman; S Pan; J Pollard; V Puri; M G Reese; K Reinert; K Remington; R D Saunders; F Scheeler; H Shen; B C Shue; I Sidén-Kiamos; M Simpson; M P Skupski; T Smith; E Spier; A C Spradling; M Stapleton; R Strong; E Sun; R Svirskas; C Tector; R Turner; E Venter; A H Wang; X Wang; Z Y Wang; D A Wassarman; G M Weinstock; J Weissenbach; S M Williams; K C Worley; D Wu; S Yang; Q A Yao; J Ye; R F Yeh; J S Zaveri; M Zhan; G Zhang; Q Zhao; L Zheng; X H Zheng; F N Zhong; W Zhong; X Zhou; S Zhu; X Zhu; H O Smith; R A Gibbs; E W Myers; G M Rubin; J C Venter
Journal:  Science       Date:  2000-03-24       Impact factor: 47.728
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  66 in total

1.  Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.

Authors:  Nathaniel Echols; Paul Harrison; Suganthi Balasubramanian; Nicholas M Luscombe; Paul Bertone; Zhaolei Zhang; Mark Gerstein
Journal:  Nucleic Acids Res       Date:  2002-06-01       Impact factor: 16.971

2.  Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.

Authors:  Zhaolei Zhang; Paul M Harrison; Yin Liu; Mark Gerstein
Journal:  Genome Res       Date:  2003-12       Impact factor: 9.043

3.  Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species.

Authors:  Daniel Dieringer; Christian Schlötterer
Journal:  Genome Res       Date:  2003-10       Impact factor: 9.043

4.  Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes.

Authors:  Zhaolei Zhang; Mark Gerstein
Journal:  Nucleic Acids Res       Date:  2003-09-15       Impact factor: 16.971

5.  The power of detecting enriched patterns: an HMM approach.

Authors:  Zhiyuan Zhai; Shih-Yen Ku; Yihui Luan; Gesine Reinert; Michael S Waterman; Fengzhu Sun
Journal:  J Comput Biol       Date:  2010-04       Impact factor: 1.479

Review 6.  Statistical signals in bioinformatics.

Authors:  Samuel Karlin
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-12       Impact factor: 11.205

7.  Likelihoods from summary statistics: recent divergence between species.

Authors:  Scotland C Leman; Yuguo Chen; Jason E Stajich; Mohamed A F Noor; Marcy K Uyenoyama
Journal:  Genetics       Date:  2005-09-02       Impact factor: 4.562

8.  Global mRNA stability is not associated with levels of gene expression in Drosophila melanogaster but shows a negative correlation with codon bias.

Authors:  Hans K Stenøien; Wolfgang Stephan
Journal:  J Mol Evol       Date:  2005-07-21       Impact factor: 2.395

9.  "Word" preference in the genomic text and genome evolution: different modes of n-tuplet usage in coding and noncoding sequences.

Authors:  Christoforos Nikolaou; Yannis Almirantis
Journal:  J Mol Evol       Date:  2005-07-19       Impact factor: 2.395

10.  Circuit assemblages derived from net dinucleotide values provide a succinct identity for the HIV-1 genome and each of its genes.

Authors:  Dorothy M Lang
Journal:  Virus Genes       Date:  2007-11-07       Impact factor: 2.332
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