Skew in CG content near the transcription start site in Arabidopsis thaliana

We have discovered a novel statistical feature of Arabidopsis thaliana genome that remarkably correlates with a position of transcription start site--CG skew peak. We hypothesize that the phenomenon can be explained by the higher mutability of unprotected cytosines.

[1]  A. Grigoriev Strand-specific compositional asymmetries in double-stranded DNA viruses. , 1999, Virus research.

[2]  B. J. Hinnebusch,et al.  Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids. , 2000, Genome research.

[3]  A. Bhagwat,et al.  Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[4]  The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[5]  S Karlin,et al.  Genome-scale compositional comparisons in eukaryotes. , 2001, Genome research.

[6]  Philipp Bucher,et al.  The Eukaryotic Promoter Database EPD , 1998, Nucleic Acids Res..

[7]  Genome Arithmetic , 1998, Science.

[8]  Temple F. Smith,et al.  Patterns of Genome Organization in Bacteria , 1998, Science.

[9]  M. Q. Zhang,et al.  Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Michael Ruogu Zhang,et al.  CART classification of human 5' UTR sequences. , 2000, Genome research.

[11]  A Grigoriev,et al.  Mutations induced by bacteriophage T7 RNA polymerase and their effects on the composition of the T7 genome. , 2000, Journal of molecular biology.

[12]  O. Lichtarge,et al.  Bacterial Mode of Replication with Eukaryotic-Like Machinery in a Hyperthermophilic Archaeon , 2000 .

[13]  S. Karlin,et al.  Strand compositional asymmetry in bacterial and large viral genomes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[14]  S. Karlin,et al.  Predicted Highly Expressed Genes of Diverse Prokaryotic Genomes , 2000, Journal of bacteriology.

[15]  A Grigoriev,et al.  Analyzing genomes with cumulative skew diagrams. , 1998, Nucleic acids research.

[16]  David J. Galas,et al.  The interaction of RNA polymerase and lac repressor with the lac control region , 1979, Nucleic Acids Res..

[17]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[18]  Anatoly S. Frolov,et al.  Prediction of eukaryotic mRNA translational properties , 1999, Bioinform..