Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes

• Published in: Nucleic acids research 2004-01, Vol.32 (17), p.4969-4978
• Main Authors: Touchon, M, Arneodo, A, d'Aubenton-Carafa, Y, Thermes, C
• Format: Article
• Language: English
• Subjects: alternative splicing; Animals; Arabidopsis - genetics; Arabidopsis thaliana; Biological Physics; Caenorhabditis elegans; Caenorhabditis elegans - genetics; DNA Repair; Drosophila melanogaster; Drosophila melanogaster - genetics; gene skew profiles; Genome; intron skew profiles; Introns; Invertebrates - genetics; Mammals - genetics; messenger RNA; Mutation; Physics; pre-messenger RNA; RNA Splicing; Sequence Analysis, DNA; transcription (genetics); Transcription, Genetic; Vertebrates - genetics
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkh823

Under no-strand bias conditions, each genomic DNA strand should present equimolarities of A and T and of G and C. Deviations from these rules are attributed to asymmetric properties intrinsic to DNA mutation–repair processes. In bacteria, strand biases are associated with replication or transcription. In eukaryotes, recent studies demonstrate that human genes present transcription-coupled biases that might reflect transcription-coupled repair processes. Here, we study strand asymmetries in intron sequences of evolutionarily distant eukaryotes, and show that two superimposed intron biases can be distinguished. (i) Biases that are maximum at intron extremities and decrease over large distances to zero values in internal regions, possibly reflecting interactions between pre-mRNA and splicing machinery; these extend over ∼0.5 kb in mammals and Arabidopsis thaliana, and over 1 kb in Caenorhabditis elegans and Drosophila melanogaster. (ii) Biases that are constant along introns, possibly associated with transcription. Strikingly, in C.elegans, these latter biases extend over intergenic regions that separate co-oriented genes. When appropriately examined, all genomes present transcription-coupled excess of T over A in the coding strand. On the opposite, GC skews are either positive (mammals, plants) or negative (invertebrates). These results suggest that transcription-coupled asymmetries result from mutation–repair mechanisms that differ between vertebrates and invertebrates.