Genome-scale compositional comparisons in eukaryotes.

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.

[1]  S. Karlin,et al.  Dinucleotide relative abundance extremes: a genomic signature. , 1995, Trends in genetics : TIG.

[2]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[3]  Stephen M. Mount,et al.  The genome sequence of Drosophila melanogaster. , 2000, Science.

[4]  S Karlin,et al.  Comparisons of eukaryotic genomic sequences. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[5]  H. Echols,et al.  Fidelity mechanisms in DNA replication. , 1991, Annual review of biochemistry.

[6]  S Karlin,et al.  Similarities and dissimilarities of phage genomes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[7]  G. Russell,et al.  Similarity of the general designs of protochordates and invertebrates , 1977, Nature.

[8]  J. Berg.  Genome sequence of the nematode C. elegans: a platform for investigating biology. , 1998, Science.

[9]  R. Elton,et al.  Doublet frequency analysis of fractionated vertebrate nuclear DNA. , 1976, Journal of molecular biology.

[10]  Melanie E. Goward,et al.  The DNA sequence of human chromosome 22 , 1999, Nature.

[11]  Alexander Bolshoy,et al.  CC dinucleotides contribute to the bending of DNA in chromatin , 1995, Nature Structural Biology.

[12]  S. Karlin,et al.  Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Andrew Smith.  Genome sequence of the nematode C-elegans: A platform for investigating biology , 1998 .

[14]  A. Krieg,et al.  The role of CpG dinucleotides in DNA vaccines. , 1998, Trends in microbiology.

[15]  Eugen C. Buehler,et al.  Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana , 1999, Nature.

[16]  S. Cross,et al.  CpG islands and genes. , 1995, Current opinion in genetics & development.

[17]  M. Hattori,et al.  The DNA sequence of human chromosome 21 , 2000, Nature.

[18]  S Karlin,et al.  Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses? , 1994, Journal of virology.

[19]  S. Karlin,et al.  Global dinucleotide signatures and analysis of genomic heterogeneity. , 1998, Current opinion in microbiology.

[20]  S Karlin,et al.  Compositional differences within and between eukaryotic genomes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J A Koziol,et al.  Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[22]  M. Cotton,et al.  Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana , 1999, Nature.

[23]  T. Kunkel.  Biological asymmetries and the fidelity of eukaryotic DNA replication , 1992, BioEssays : news and reviews in molecular, cellular and developmental biology.