Skip to main content
SpringerLink
Log in

Strand compositional asymmetries in vertebrate large genes

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Both transcription-associated and replication-associated strand compositional asymmetries have recently been shown in vertebrate genomes. In this paper, we illustrate that transcription-associated strand compositional asymmetries and replication-associated ones coexist in most vertebrate large genes, although in most case the former conceals the latter. Furthermore, we found that the transcription-associated strand compositional asymmetries of housekeeping genes are stronger than those of somatic cell expressed genes. Together with other evidence, we suggest that germline transcription-associated strand asymmetric mutations may be the main cause of the transcription-associated strand compositional asymmetries.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Abbreviations

CSD:

Cumulative skew diagram

CSDD:

Cumulative skew difference diagram

References

  1. Lobry JR (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13(5):660–665

    PubMed  CAS  Google Scholar 

  2. Francino MP, Ochman H (1997) Strand asymmetries in DNA evolution. Trends Genet 13(6):240–245

    Article  PubMed  CAS  Google Scholar 

  3. Grigoriev A (1998) Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res 26(10):2286–2290

    Article  PubMed  CAS  Google Scholar 

  4. Mrazek J, Karlin S (1998) Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA 95(7):3720–3725

    Article  PubMed  CAS  Google Scholar 

  5. Reyes A, Gissi C, Pesole G, Saccone C (1998) Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol Biol Evol 15(8):957–966

    PubMed  CAS  Google Scholar 

  6. Frank AC, Lobry JR (1999) Asymmetric substitution patterns: A review of possible underlying mutational or selective mechanisms. Gene 238(1):65–77

    Article  PubMed  CAS  Google Scholar 

  7. Grigoriev A (1999) Strand-specific compositional asymmetries in double-stranded DNA viruses. Virus Res 60(1):1–19

    Article  PubMed  CAS  Google Scholar 

  8. Rocha EPC, Danchin A, Viari A (1999) Universal replication biases in bacteria Mol Microbiol 32(1):11–16

    Article  PubMed  CAS  Google Scholar 

  9. Lobry JR, Sueoka N (2002) Asymmetric directional mutation pressures in bacteria. Genome Biol 3(10): research0058.0051–0058.0014

  10. Tillier ERM, Collins RA (2000) The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol 50(3):249–257

    PubMed  CAS  Google Scholar 

  11. Kowalczuk M, Mackiewicz P, Mackiewicz D, Nowicka A, Dudkiewicz M, Dudek MR, Cebrat S (2001) DNA asymmetry and the replicational mutational pressure. J Appl Genet 42(4):553–577

    PubMed  CAS  Google Scholar 

  12. Beletskii A, Bhagwat AS (1998) Correlation between transcription and C to T mutations in the non-transcribed DNA strand. Biol Chem 379(4–5):549–551

    PubMed  CAS  Google Scholar 

  13. Francino MP, Ochman H (2001) Deamination as the basis of strand-asymmetric evolution in transcribed Escherichia coli sequences. Mol Biol Evol 18(6):1147–1150

    PubMed  CAS  Google Scholar 

  14. Zeigler DR, Dean DH (1990) Orientation of genes in the Bacillus subtilis chromosome. Genetics 125(4):703–708

    PubMed  CAS  Google Scholar 

  15. McLean MJ, Wolfe KH, Devine KM (1998) Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J Mol Evol 47(6):691–696

    Article  PubMed  CAS  Google Scholar 

  16. Rocha EP, Danchin A (2003) Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nat Genet 34(4):377–378

    Article  PubMed  CAS  Google Scholar 

  17. Baran RH, Ko H (2006) An Ising model of transcription polarity in bacterial chromosomes. Physica A 362(2):403–422

    Article  Google Scholar 

  18. Nikolaou C, Almirantis Y (2005) A study on the correlation of nucleotide skews and the positioning of the origin of replication: different modes of replication in bacterial species. Nucleic Acids Res 33(21):6816–6822

    Article  PubMed  CAS  Google Scholar 

  19. Baran RH, Ko H, Jernigan RW (2003) Methods for comparing sources of strand compositional asymmetry in microbial chromosomes. DNA Res 10(3):85–95

    Article  PubMed  CAS  Google Scholar 

  20. Green P, Ewing B, Miller W, Thomas PJ, Green ED (2003) Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet 33(4):514–517

    Article  PubMed  CAS  Google Scholar 

  21. Majewski J (2003) Dependence of mutational asymmetry on gene-expression levels in the human genome. Am J Hum Genet 73(3):688–692

    Article  PubMed  CAS  Google Scholar 

  22. Niu DK, Lin K, Zhang DY (2003) Strand compositional asymmetries of nuclear DNA in eukaryotes. J Mol Evol 57(3):325–334

    Article  PubMed  CAS  Google Scholar 

  23. Touchon M, Nicolay S, Audit B, Brodie of Brodie E-B, d’Aubenton-Carafa Y, Arneodo A, Thermes C (2005) Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. Proc Natl Acad Sci USA 102(28):9836–9841

    Article  PubMed  CAS  Google Scholar 

  24. Brodie of Brodie E-B, Nicolay S, Touchon M, Audit B, d’Aubenton-Carafa Y, Thermes C, Arneodo A (2005) From DNA sequence analysis to modeling replication in the human genome. Phys Rev Lett 9424(24):248103

    Article  CAS  Google Scholar 

  25. Hou WR, Wang HF, Niu DK (2006) Replication-associated strand asymmetries in vertebrate genomes and implications for replicon size, DNA replication origin, and termination. Biochem Biophys Res Commun 344(4):1258–1262

    Article  PubMed  CAS  Google Scholar 

  26. Touchon M, Nicolay S, Arneodo A, d’Aubenton-Carafa Y, Thermes C (2003) Transcription-coupled TA and GC strand asymmetries in the human genome. FEBS Lett 555(3):579–582

    Article  PubMed  CAS  Google Scholar 

  27. Touchon M, Arneodo A, d’Aubenton-Carafa Y, Thermes C (2004) Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Nucleic Acids Res 32(17):4969–4978

    Article  PubMed  CAS  Google Scholar 

  28. Chamary JV, Parmley JL, Hurst LD (2006) Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7(2):98–108

    Article  PubMed  CAS  Google Scholar 

  29. Parmley JL, Chamary JV, Hurst LD (2006) Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol 23(2):301–309

    Article  PubMed  CAS  Google Scholar 

  30. Pozzoli U, Riva L, Menozzi G, Cagliani R, Comi GP, Bresolin N, Giorda R, Sironi M (2004) Over-representation of exonic splicing enhancers in human intronless genes suggests multiple functions in mRNA processing. Biochem Biophys Res Commun 322(2):470–476

    Article  PubMed  CAS  Google Scholar 

  31. Lobry JR (1996) A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie 78(5):323–326

    Article  PubMed  CAS  Google Scholar 

  32. Zhang R, Zhang C-T (2005) Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea 1(5):335–346

    Article  PubMed  CAS  Google Scholar 

  33. Lewin B (2004) Genes, VIII edn. Pearson Prentice Hall, Upper Saddle River

  34. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G et al (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101(16):6062–6067

    Article  PubMed  CAS  Google Scholar 

  35. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A et al (2002) Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 99(7):4465–4470

    Article  PubMed  CAS  Google Scholar 

  36. Karlin S, Campbell AM, Mrazek J (1998) Comparative DNA analysis across diverse genomes. Annu Rev Genet 32:185–225

    Article  PubMed  CAS  Google Scholar 

  37. Gierlik A, Kowalczuk M, Mackiewicz P, Dudek MR, Cebrat S (2000) Is there replication-associated mutational pressure in the Saccharomyces cerevisiae genome? J Theor Biol 202(4):305–314

    Article  PubMed  CAS  Google Scholar 

  38. Chelly J, Concordet JP, Kaplan JC, Kahn A (1989) Illegitimate transcription: transcription of any gene in any cell type. Proc Natl Acad Sci USA 86(8): 2617–2621

    Article  PubMed  CAS  Google Scholar 

  39. Kimoto Y (1998) A single human cell expresses all messenger ribonucleic acids: the arrow of time in a cell. Mol Gen Genet 258(3):233–239

    Article  PubMed  CAS  Google Scholar 

  40. Sarkar G, Sommer SS (1989) Access to a messenger RNA sequence or its protein product is not limited by tissue or species specificity. Science 244(4902):331–334

    Article  PubMed  CAS  Google Scholar 

  41. Niu D-K (2005) Low-level illegitimate transcription of genes may be to silence the genes. Biochem Biophys Res Commun 337(2):413–414

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We thank Lei Zhu and Shu-Wei Li for technical helps. This work was supported by the National Natural Science Foundation of China (30270695) and Beijing Normal University.

Author information

Author notes

  1. Wen-Ru Hou

    Present address: National Institute of Biological Sciences, Beijing, 102206, China

Authors and Affiliations

  1. Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China

    Hai-Fang Wang, Wen-Ru Hou & Deng-Ke Niu

Authors
  1. Hai-Fang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wen-Ru Hou
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Deng-Ke Niu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Deng-Ke Niu.

Electronic supplementary material

Below is the link to the electronic supplementary material

ESM1 (PDF 635 kb)

ESM3 (PDF 297 kb)

ESM1 (PDF 553 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wang, HF., Hou, WR. & Niu, DK. Strand compositional asymmetries in vertebrate large genes. Mol Biol Rep 35, 163–169 (2008). https://doi.org/10.1007/s11033-007-9066-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-007-9066-6

Keywords

Search

Navigation