ArticleNucleic acids research2004
Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract.Journal of evolutionary biology · 2023Article
- Strand asymmetries across genomic processes.Computational and structural biotechnology journal · 2023Review
- Revisiting the Relationships Between Genomic G + C Content, RNA Secondary Structures, and Optimal Growth Temperature.Journal of molecular evolution · 2021Article
- Article
- Transcription-Associated Compositional Skews in Drosophila Genes.Genome biology and evolution · 2018Article
- Article
- GC skew is a conserved property of unmethylated CpG island promoters across vertebrates.Nucleic acids research · 2015Article
- Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells.Nucleic acids research · 2014Article
- Topoisomerase II regulates yeast genes with singular chromatin architectures.Nucleic acids research · 2013Article
- Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm.Nature protocols · 2013Article
- Human genome replication proceeds through four chromatin states.PLoS computational biology · 2013Article
- Linking the DNA strand asymmetry to the spatio-temporal replication program: II. Accounting for neighbor-dependent substitution rates.The European physical journal. E, Soft matter · 2012Article
- Linking the DNA strand asymmetry to the spatio-temporal replication program. I. About the role of the replication fork polarity in genome evolution.The European physical journal. E, Soft matter · 2012Article
- Incidence of genome structure, DNA asymmetry, and cell physiology on T-DNA integration in chromosomes of the phytopathogenic fungus Leptosphaeria maculans.G3 (Bethesda, Md.) · 2012Article
- Measures of compositional strand bias related to replication machinery and its applications.Current genomics · 2012Article
- Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines.PLoS computational biology · 2012Article
- Opposite GC skews at the 5' and 3' ends of genes in unicellular fungi.BMC genomics · 2011Article
- Genome-wide depletion of replication initiation events in highly transcribed regions.Genome research · 2011Article
- Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants.Nucleic acids research · 2011Article
- Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content.Genome biology · 2011Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 approximately 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.
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