Journal of Molecular Evolution

, Volume 71, Issue 5–6, pp 415–426

Intronic AT Skew is a Defendable Proxy for Germline Transcription but does not Predict Crossing-Over or Protein Evolution Rates in Drosophila melanogaster



Recent evidence suggests that germline transcription may affect both protein evolutionary rates, possibly mediated by repair processes, and recombination rates, possibly mediated by chromatin and epigenetic modification. Here, we test these propositions in Drosophila melanogaster. The challenge for such analyses is to provide defendable measures of germline gene expression. Intronic AT skew is a good candidate measure as it is thought to be a consequence, at least in part, of transcription-coupled repair. Prior evidence suggests that intronic AT skew in D.melanogaster is not affected by proximity to intron extremities and differs between transcribed DNA and flanking sequence. We now also establish that intronic AT skew is a defendable proxy for germline expression as (a) it is more similar than expected by chance between introns of the same gene (which is not accounted for by physical proximity), (b) is correlated with male germline expression, and (c) is more pronounced in broadly expressed genes. Furthermore, (d) a trend for intronic skew to differ between 3′ and 5′ ends of genes is particular to broadly expressed genes. Finally, (e) controlling for physical distance, introns of proximate genes are most different in skew if they have different tissue specificity. We find that intronic AT skew, employed as a proxy for germline transcription, correlates neither with recombination rates nor with the rate of protein evolution. We conclude that there is no prima facie evidence that germline expression modulates recombination rates or monotonically affects protein evolution rates in D. melanogaster.


Drosophila melanogaster Germline expression Somatic gene expression Tissue specificity Recombination Nucleotide asymmetry Intronic AT skew 


  1. Bachtrog D (2003) Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda. Genetics 165:1221–1232PubMedGoogle Scholar
  2. Berchowitz LE, Hanlon SE, Lieb JD, Copenhaver GP (2009) A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae. Genome Res 19:2245–2257CrossRefPubMedGoogle Scholar
  3. Berglund J, Pollard KS, Webster MT (2009) Hotspots of biased nucleotide substitutions in human genes. PLoS Biol 7:e26CrossRefPubMedGoogle Scholar
  4. Betancourt AJ, Presgraves DC (2002) Linkage limits the power of natural selection in Drosophila. Proc Natl Acad Sci USA 99:13616–13620CrossRefPubMedGoogle Scholar
  5. Betancourt AJ, Welch JJ, Charlesworth (2009) Reduced effectiveness of selection caused by a lack of recombination. Curr Biol 19:655–660CrossRefPubMedGoogle Scholar
  6. Borde V, Robine N, Lin W, Bonfils S, Geli V, Nicolas A (2009) Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites. EMBO J 28:99–111CrossRefPubMedGoogle Scholar
  7. Buard J, Barthes P, Grey C, de Massy B (2009) Distinct histone modifications define initiation and repair of meiotic recombination in the mouse. EMBO J 28:2616–2624CrossRefPubMedGoogle Scholar
  8. Chintapalli VR, Wang J, Dow JA (2007) Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet 39:715–720CrossRefPubMedGoogle Scholar
  9. Comeron JM (2004) Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics 167:1293–1304CrossRefPubMedGoogle Scholar
  10. de Wit E, Braunschweig U, Greil F, Bussemaker HJ, van Steensel B (2008) Global chromatin domain organization of the Drosophila genome. PLoS Genet 4:e1000045CrossRefPubMedGoogle Scholar
  11. Duret L, Galtier N (2009) Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet 10:285–311CrossRefPubMedGoogle Scholar
  12. Duret L, Mouchiroud D (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, Arabidopsis. Proc Natl Acad Sci USA 96:4482–4487CrossRefPubMedGoogle Scholar
  13. Duret L, Mouchiroud D (2000) Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol 17:68–74PubMedGoogle Scholar
  14. Eyre-Walker A, Hurst LD (2001) The evolution of isochores. Nat Rev Genet 2:549–555CrossRefPubMedGoogle Scholar
  15. Galtier N, Duret L (2007) Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet 23:273–277CrossRefPubMedGoogle Scholar
  16. Galtier N, Duret L, Glemin S, Ranwez V (2009) GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet 25:1–5CrossRefPubMedGoogle Scholar
  17. Green P, Ewing B, Miller W, Thomas PJ, Program NCS, Green ED (2003) Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet 33:514–517CrossRefPubMedGoogle Scholar
  18. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77–88CrossRefPubMedGoogle Scholar
  19. Haddrill PR, Charlesworth B (2008) Non-neutral processes drive the nucleotide composition of non-coding sequences in Drosophila. Biol Lett 4:438–441CrossRefPubMedGoogle Scholar
  20. Haddrill PR, Waldron FM, Charlesworth B (2008) Elevated levels of expression associated with regions of the Drosophila genome that lack crossing over. Biol Lett 4:758–761CrossRefPubMedGoogle Scholar
  21. Hey J, Kliman RM (2002) Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160:595–608PubMedGoogle Scholar
  22. Huvet M, Nicolay S, Touchon M, Audit B, d’Aubenton-Carafa Y, Arneodo A, Thermes C (2007) Human gene organization driven by the coordination of replication and transcription. Genome Res 17:1278–1285CrossRefPubMedGoogle Scholar
  23. Kulathinal RJ, Bennettt SM, Fitzpatrick CL, Noor MAF (2008) Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence. Proc Natl Acad Sci USA 105:10051–10056CrossRefPubMedGoogle Scholar
  24. Larracuente AM, Sackton TB, Greenberg AJ, Wong A, Singh ND, Sturgill D, Zhang Y, Oliver B, Clark AG (2008) Evolution of protein-coding genes in Drosophila. Trends Genet 24:114–123CrossRefPubMedGoogle Scholar
  25. Lercher MJ, Urrutia AO, Hurst LD (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 31:180–183CrossRefPubMedGoogle Scholar
  26. Liao BY, Scott NM, Zhang JZ (2006) Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol Biol Evol 23:2072–2080CrossRefPubMedGoogle Scholar
  27. Majewski J (2003) Dependence of mutational asymmetry on gene-expression levels in the human genome. Am J Hum Genet 73:688–692CrossRefPubMedGoogle Scholar
  28. Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM (2008) High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454:479–485CrossRefPubMedGoogle Scholar
  29. Marais G, Mouchiroud D, Duret L (2003) Neutral effect of recombination on base composition in Drosophila. Genet Res 81:79–87CrossRefPubMedGoogle Scholar
  30. McVicker G, Green P (2010) Genomic signatures of germline gene expression. Genome Res: doi: 10.1101/gr.106666.110; Epub date 2010/08/06
  31. Mugal CF, Wolf JB, von Grunberg HH, Ellegren H (2010) Conservation of neutral substitution rate and substitutional asymmetries in mammalian genes. Genome Biol Evol 2:19–28CrossRefPubMedGoogle Scholar
  32. Nagylaki T (1983) Evolution of a finite population under gene conversion. Proc Natl Acad Sci USA 80:6278–6281CrossRefPubMedGoogle Scholar
  33. Necsulea A, Guillet C, Cadoret J-C, Prioleau M-N, Duret L (2009a) The relationship between DNA replication and human genome organization. Mol Biol Evol 26:729–741CrossRefPubMedGoogle Scholar
  34. Necsulea A, Semon M, Duret L, Hurst LD (2009b) Monoallelic expression and tissue specificity are associated with high crossover rates. Trends Genet 25:519–522CrossRefPubMedGoogle Scholar
  35. Pal C, Papp B, Hurst LD (2001) Highly expressed genes in yeast evolve slowly. Genetics 158:927–931PubMedGoogle Scholar
  36. Parmley JL, Urrutia AO, Potrzebowski L, Kaessmann H, Hurst LD (2007) Splicing and the evolution of proteins in mammals. PLoS Biol 5:343–353CrossRefGoogle Scholar
  37. Polak P, Arndt PF (2008) Transcription induces strand-specific mutations at the 5′ end of human genes. Genome Res 18:1216–1223CrossRefPubMedGoogle Scholar
  38. Powell JR, Moriyama EN (1997) Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci USA 94:7784–7790CrossRefPubMedGoogle Scholar
  39. Presgraves DC (2005) Recombination enhances protein adaptation in Drosophila melanogaster. Curr Biol 15:1651–1656CrossRefPubMedGoogle Scholar
  40. Sigurdsson MI, Smith AV, Bjornsson HT, Jonsson JJ (2009) HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination. Genome Res 19:581–589CrossRefPubMedGoogle Scholar
  41. Singh ND, Aquadro CF, Clark AG (2009) Estimation of fine-scale recombination intensity variation in the white-echinus interval of D. melanogaster. J Mol Evol 69:42–53CrossRefPubMedGoogle Scholar
  42. Spellman PT, Rubin GM (2002) Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 1:5CrossRefPubMedGoogle Scholar
  43. Sun M, Hurst LD, Carmichael GG, Chen J (2005) Evidence for a preferential targeting of 3′-UTRs by cis-encoded natural antisense transcripts. Nucleic Acids Res 33:5533–5543CrossRefPubMedGoogle Scholar
  44. Sun M, Hurst LD, Carmichael GG, Chen J (2006) Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcription and organismic complexity. Genome Res 16:922–933CrossRefPubMedGoogle Scholar
  45. Svejstrup JQ (2002) Mechanisms of transcription-coupled DNA repair. Nat Rev Mol Cell Biol 3:21–29CrossRefPubMedGoogle Scholar
  46. Takano-Shimizu T (2001) Local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes. Mol Biol Evol 18:606–619PubMedGoogle Scholar
  47. Touchon M, Arneodo A, d’Aubenton-Carafa Y, Thermes C (2004) Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Nucleic Acids Res 32:4969–4978CrossRefPubMedGoogle Scholar
  48. Touchon M, Nicolay S, Audit B, Brodie of Brodie EB, 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 102:9836–9841CrossRefPubMedGoogle Scholar
  49. Vibranovski MD, Lopes HF, Karr TL, Long M (2009) Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genes. PLoS Genet 5:e1000731CrossRefPubMedGoogle Scholar
  50. Warnecke T, Hurst LD (2007) Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster. Mol Biol Evol 24:2755–2762CrossRefPubMedGoogle Scholar
  51. Warnecke T, Parmley JL, Hurst LD (2008) Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes. Genome Biol 9:R29CrossRefPubMedGoogle Scholar
  52. Weber CC, Hurst LD (2009) Protein rates of evolution are predicted by double-strand break events, independent of crossing-over rates. Genome Biol Evol 1:340–349CrossRefPubMedGoogle Scholar
  53. Webster MT, Smith NG, Lercher MJ, Ellegren H (2004) Gene expression, synteny, and local similarity in human noncoding mutation rates. Mol Biol Evol 21:1820–1830CrossRefPubMedGoogle Scholar
  54. Wu TC, Lichten M (1994) Meiosis-induced double-strand break sites determined by yeast chromatin structure. Science 263:515–518CrossRefPubMedGoogle Scholar
  55. Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, Bar-Even A, Horn-Saban S, Safran M, Domany E, Lancet D, Shmueli O (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21:650–659CrossRefPubMedGoogle Scholar
  56. Yang L, Yu J (2009) A comparative analysis of divergently-paired genes (DPGs) among Drosophila and vertebrate genomes. BMC Evol Biol 9:55CrossRefPubMedGoogle Scholar
  57. Zhang Z, Parsch J (2005) Positive correlation between evolutionary rate and recombination rate in Drosophila genes with male-biased expression. Mol Biol Evol 22:1945–1947CrossRefPubMedGoogle Scholar
  58. Zhang Z, Hambuch TM, Parsch J (2004) Molecular evolution of sex-biased genes in Drosophila. Mol Biol Evol 21:2130–2139CrossRefPubMedGoogle Scholar
  59. Zhang Y, Sturgill D, Parisi M, Kumar S, Oliver B (2007) Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature 450:233–237CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Department of Biology and BiochemistryUniversity of BathBathUK

Personalised recommendations