Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements

eLife

Volumn 2015, Issue 4, 2015, Pages

  Ellison, Christopher E ^a   Bachtrog, Doris ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING AFFINITY; CHROMATIN IMMUNOPRECIPITATION; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA MIRANDA; GENE CONVERSION; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENE INSERTION; GENE INTERACTION; GENE MUTATION; GENE REGULATORY NETWORK; GENE SEQUENCE; GENETIC POLYMORPHISM; NONHUMAN; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; TRANSGENICS; TRANSPOSON; X CHROMOSOME; ALLELE; ANIMAL; GENETICS; HAPLOTYPE; MOLECULAR EVOLUTION; MUTATION; NUCLEOTIDE MOTIF; REGULATORY SEQUENCE;

PROTEIN BINDING; TRANSPOSON;

ALLELES; ANIMALS; DNA TRANSPOSABLE ELEMENTS; DROSOPHILA; EVOLUTION, MOLECULAR; GENE CONVERSION; HAPLOTYPES; MUTAGENESIS, INSERTIONAL; MUTATION; NUCLEOTIDE MOTIFS; PROTEIN BINDING; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 85003047870     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.05899     Document Type: Article

References (31)

1. Alekseyenko, A. A., Ellison, C. E., Gorchakov, A. A., Zhou, Q., Kaiser, V. B., Toda, N., Walton, Z., Peng, S., Park, P. J., Bachtrog, D., et al. (2013). Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila. Genes Dev 27, 853-858.
2. Alekseyenko, A. A., Peng, S., Larschan, E., Gorchakov, A. A., Lee, O. K., Kharchenko, P., McGrath, S. D., Wang, C. I., Mardis, E. R., Park, P. J., et al. (2008). A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 134, 599-609.
3. Arguello, J. R., Chen, Y., Yang, S., Wang, W., and Long, M. (2006). Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila. PLoS Genet 2, 745-754.
4. Bachtrog, D., and Charlesworth, B. (2002). Reduced adaptation of a non-recombining neo-Y chromosome. Nature 416, 323-326.
5. Bateman, J. R., Lee, A. M., and Wu, C. T. (2006). Site-specific transformation of Drosophila via phiC31 integrase-mediated cassette exchange. Genetics 173, 769-777.
6. Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature (London) 456, 53-59.
7. Bone, J. R., and Kuroda, M. I. (1996). Dosage compensation regulatory proteins and the evolution of sex chromosomes in Drosophila. Genetics 144, 705-713.
8. Bradley, R. K., Roberts, A., Smoot, M., Juvekar, S., Do, J., Dewey, C., Holmes, I., and Pachter, L. (2009). Fast statistical alignment. PLoS Comput Biol 5, e1000392.
9. Carvalho, A. B., and Clark, A. G. (2005). Y chromosome of D. pseudoobscura is not homologous to the ancestral Drosophila Y. Science 307, 108-110.
10. Chen, J.-M., Cooper, D. N., Chuzhanova, N., Ferec, C., and Patrinos, G. P. (2007). Gene conversion: mechanisms, evolution and human disease. Nature Reviews Genetics 8, 762-775.
11. Cowley, M., and Oakey, R. J. (2013). Transposable elements re-wire and fine-tune the transcriptome. PLoS Genet 9, e1003234.
12. Eickbush, T. H., and Eickbush, D. G. (2007). Finely orchestrated movements: Evolution of the ribosomal RNA genes. Genetics 175, 477-485.
13. Ellison, C. E., and Bachtrog, D. (2013). Dosage Compensation via Transposable Element Mediated Rewiring of a Regulatory Network. Science (Washington D C) 342, 846-850.
14. Ellison, C. E. and Bachtrog, D. (2015) Data from: Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements. Dryad Digital Repository. doi: 10. 5061/dryad. dg483.
15. Feschotte, C. (2008). Transposable elements and the evolution of regulatory networks. Nature Reviews Genetics 9, 397-405.
16. Hall, G. S., and Little, D. P. (2007). Relative quantitation of virus population size in mixed genotype infections using sequencing chromatograms. Journal of Virological Methods 146, 22-28.
17. Langmead, B., and Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359.
18. Mano, S., and Innan, H. (2008). The evolutionary rate of duplicated genes under concerted evolution. Genetics 180, 493-505.
19. Mansai, S. P., and Innan, H. (2010). The Power of the Methods for Detecting Interlocus Gene Conversion. Genetics 184, 517-U292.
20. Marin, I., Franke, A., Bashaw, G. J., and Baker, B. S. (1996). The dosage compensation system of Drosophila is coopted by new evolved X chromosomes. Nature 383, 160-163.
21. Ohta, T. (2010). Gene conversion and evolution of gene families: an overview. Genes (Basel) 1, 349-356.
22. Peng, Y., Leung, H. C. M., Yiu, S. M., and Chin, F. Y. L. (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics (Oxford) 28, 1420-1428.
23. Polavarapu, N., Marino-Ramirez, L., Landsman, D., McDonald, J. F., and Jordan, I. K. (2008). Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics 9, Article No.: 226.
24. Richards, S., Liu, Y., Bettencourt, B. R., Hradecky, P., Letovsky, S., Nielsen, R., Thornton, K., Hubisz, M. J., Chen, R., Meisel, R. P., et al. (2005). Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res 15, 1-18.
25. Rozen, S., Skaletsky, H., Marszalek, J. D., Minx, P. J., Cordum, H. S., Waterston, R. H., Wilson, R. K., and Page, D. C. (2003). Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature (London) 423, 873-876.
26. Sasaki, M., Lange, J., and Keeney, S. (2010). Genome destabilization by homologous recombination in the germ line. Nature Reviews Molecular Cell Biology 11, 182-195.
27. Stewart, A. J., Hannenhalli, S., and Plotkin, J. B. (2013). Why Transcription Factor Binding Sites Are Ten Nucleotides Long. Genetics 193.
28. Straub, T., Grimaud, C., Gilfillan, G. D., Mitterweger, A., and Becker, P. B. (2008). The Chromosomal High-Affinity Binding Sites for the Drosophila Dosage Compensation Complex. PLoS Genet 4, Article No.: e1000302.
29. Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M., and Barton, G. J. (2009). Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics (Oxford) 25, 1189-1191.
30. Zangenberg, G., Huang, M.-M., Arnheim, N., and Erlich, H. (1995). New HLA-DPB1 alleles generated by interallelic gene conversion detected by analysis of sperm. Nat Genet 10, 407-414.
31. Zhou, Q., Ellison, C. E., Kaiser, V. B., Alekseyenko, A. A., Gorchakov, A. A., and Bachtrog, D. (2013). The Epigenome of Evolving Drosophila Neo-Sex Chromosomes: Dosage Compensation and Heterochromatin Formation. PLoS Biology 11, Article No.: e1001711.