Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 17, 2009, Pages 7079-7082

  Assis, Raquel ^a   Kondrashov, Alexey S ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Arms race; Molecular evolution; Positive selection; Small RNA

Indexed keywords

PIWI PROTEIN; RNA; SMALL INTERFERING RNA;

ANIMAL EXPERIMENT; ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; DNA FLANKING REGION; EVOLUTION; GENE INSERTION; GENETIC VARIABILITY; MAMMAL; MOUSE; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PRIMATE; PRIORITY JOURNAL; RAT; TRANSPOSON; ANIMAL; GENETIC RECOMBINATION; GENETICS; MOLECULAR EVOLUTION; TIME;

MAMMALIA; PRIMATES; RATTUS; RODENTIA;

ANIMALS; EVOLUTION, MOLECULAR; GENETIC VARIATION; MICE; MULTIGENE FAMILY; RATS; RECOMBINATION, GENETIC; RNA, SMALL INTERFERING; TIME FACTORS;

EID: 66349118913     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0900523106     Document Type: Article

References (27)

1. Sontheimer EJ, Carthew RW (2005) Silence from within: Endogenous siRNAs and miRNAs. Cell 122:9-12.
2. Aravin AA, Hannon GJ, Brennecke J (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318:761-764.
3. Shabalina SA, Koonin EV (2008) Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol 23:578-587.
4. Lau NC, et al. (2006) Characterization of the piRNA complex from rat testes. Science 313:363-367.
5. Girard A, Sachidanandam R, Hannon GJ, Carmell MA (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442:199-202.
6. Aravin AA, et al. (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442:203-207.
7. Watanabe T, et al. (2006) Identification and characterization of two novel classes of small RNAs in the mouse germline: Retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev 20:1732-1743.
8. Grivna ST, Beyret E, Wang Z, Lin H (2006) A novel class of small RNAs in mouse spermatogenic cells. Genes Dev 20:1709-1714.
9. Lynch M (2007) in The Origins of Genome Architecture, eds Lynch M (Sinauer Associates, Sunderland, MA), pp 197-202.
10. Betel D, Sheridan R, Marks DS, Sander C (2007) Computational analysis of mouse piRNA sequence and biogenesis. PLoS Comp Biol 3:2219-2227.
11. Cusack BP, Wolfe KH (2006) Not born equal: Increased rate asymmetry in relocated and retrotransposed rodent gene duplicates. Mol Biol Evol 24:679-686.
12. Yang S, et al. (2008) Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. PLoS Genet 4:78-87.
13. Lupski JR, Stankiewicz P (2005) Genomic disorders: Molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet 1:627-633.
14. Kwan-Wood GL, Jeffreys AJ (2007) Processes of de novo duplication of human β-globin genes. Proc Natl Acad Sci USA 104:10950-10955.
15. Lichten M, Haber JE (1989) Position effects in ectopic and allelic mitotic recombination in Saccharomyces cerevisiae. Genetics 123:261-268.
16. Nimura Y, Nei M (2005) Evolutionary changes of the number of olfactory receptor genes in the human and mouse lineages. Gene 346:23-28.
17. Lu J, et al. (2008) The birth and death of microRNA genes in Drosophila. Nat Genet 40:351-355.
18. Lupski JR (2007) Genomic rearrangements and sporadic disease. Nat Genet 39:S43-S47.
19. Kondrashov FA, Kondrashov AS (2006) Role of selection in fixation of gene duplications. J Theor Biol 239:141-151.
20. Smith NGC, Eyre-Walker A (2002) Adaptive protein evolution in Drosophila. Nature 415:1022-1024.
21. Guryev V, et al. (2008) Distribution and functional impact of DNA copy number variation in the rat. Nat Genet 40:538-545.
22. Graubert TA, et al. (2007) A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet 3:21-29.
23. She X, Cheng Z, Zollner S, Church DM, Eichler EE (2008) Mouse segmental duplication and copy number variation. Nat Genet 40:909-914.
24. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2008) GenBank. Nucleic Acids Res 36:D25-D30.
25. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
26. Ogurtsov AY, Roytberg MA, Shabalina SA, Kondrashov AS (2002) OWEN: Aligning long collinear regions of genomes. Bioinformatics 18:1703-1704.
27. Karolchik D, et al. (2008) The UCSC Genome Browser Database: Update. Nucleic Acids Res 36:D773-D779.