Inference of Transposable Element Ancestry

English version České info

The most common entities in vertebrate genomes are transposable elements (TEs), DNA sequences that have been repeatedly copied and inserted into new locations throughout the genome. Some TEs have been replicated hundreds of thousands of times, and their ecology and evolutionary history within a genome is thus critical to understanding how genome structure evolves. It was once thought that only a few “master gene” copies could replicate, while the rest were inactive (dead on arrival), but recent computational and laboratory studies have indicated that this is not the case. However, previous methods for reconstructing TE evolutionary history were not designed to solve the problem of determining the ancestral source sequence for large numbers of elements. Here, we present a new method that is. Our method surveys all likely TE ancestors and determines the probability that each modern element arose from each of its plausible ancestors. We applied our method to the gibbon-derived LAVA TE family and to the human AluSc subfamily and inferred many more source elements than indicated by previous methods. This new method will help us better understand TE evolution, including both the impact of sequence on replication and the substitution process after replication.

Vyšlo v časopise: Inference of Transposable Element Ancestry. PLoS Genet 10(8): e32767. doi:10.1371/journal.pgen.1004482
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004482

Souhrn

Zdroje

1. De KoningAPJ, GuW, CastoeTA, BatzerMA, PollockDD (2011) Repetitive Elements May Comprise Over Two-Thirds of the Human Genome. PLoS Genet 7: e1002384 doi:10.1371/journal.pgen.1002384

2. WillardC, NguyenHT, SchmidCW (1987) Existence of at least three distinct Alu subfamilies. J Mol Evol 26: 180–186 doi:10.1007/BF02099850

3. KidoY, HimbergM, TakasakiN, OkadaN (1994) Amplification of Distinct Subfamilies of Short Interspersed Elements During Evolution of the Salmonidae. J Mol Biol 241: 633–644 doi:10.1006/jmbi.1994.1540

4. JurkaJ, SmithT (1988) A fundamental division in the Alu family of repeated sequences. Proc Natl Acad Sci U S A 85: 4775–4778.

5. SlagelV, FlemingtonE, Traina-DorgeV, BradshawH, DeiningerP (1987) Clustering and subfamily relationships of the Alu family in the human genome. Mol Biol Evol 4: 19–29.

6. KraneDE, ClarkAG, ChengJF, HardisonRC (1991) Subfamily relationships and clustering of rabbit C repeats. Mol Biol Evol 8: 1–30.

7. QuentinY (1989) Successive waves of fixation of B1 variants in rodent lineage history. J Mol Evol 28: 299–305 doi:10.1007/BF02103425

8. ShenMR, BatzerMA, DeiningerPL (1991) Evolution of the master Alu gene(s). J Mol Evol 33: 311–320 doi:10.1007/BF02102862

9. DeiningerPL, BatzerMA, HutchisonCA3rd, EdgellMH (1992) Master genes in mammalian repetitive DNA amplification. Trends Genet TIG 8: 307–311.

10. CordauxR, HedgesDJ, BatzerMA (2004) Retrotransposition of Alu elements: how many sources? Trends Genet 20: 464–467 doi:10.1016/j.tig.2004.07.012

11. BrookfieldJFY, JohnsonLJ (2006) The Evolution of Mobile DNAs: When Will Transposons Create Phylogenies That Look As If There Is a Master Gene? Genetics 173: 1115–1123 doi:10.1534/genetics.104.027219

12. CordauxR, BatzerMA (2009) The impact of retrotransposons on human genome evolution. Nat Rev Genet 10: 691–703 doi:10.1038/nrg2640

13. BennettEA, KellerH, MillsRE, SchmidtS, MoranJV, et al. (2008) Active Alu retrotransposons in the human genome. Genome Res 18: 1875–1883 doi:10.1101/gr.081737.108

14. ArndtPF, PetrovDA, HwaT (2003) Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation. Mol Biol Evol 20: 1887–1896 doi:10.1093/molbev/msg204

15. BandeltHJ, ForsterP, RöhlA (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37–48.

16. FelsensteinJ (1978) Cases in which Parsimony or Compatibility Methods will be Positively Misleading. Syst Biol 27: 401–410 doi:10.1093/sysbio/27.4.401

17. XiongY, EickbushTH (1988) Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol Biol Evol 5: 675–690.

18. KordisD, GubensekF (1997) Bov-B long interspersed repeated DNA (LINE) sequences are present in Vipera ammodytes phospholipase A2 genes and in genomes of Viperidae snakes. Eur J Biochem FEBS 246: 772–779.

19. CarboneL, HarrisRA, MootnickAR, MilosavljevicA, MartinDIK, et al. (2012) Centromere Remodeling in Hoolock leuconedys (Hylobatidae) by a New Transposable Element Unique to the Gibbons. Genome Biol Evol 4: 760–770 doi:10.1093/gbe/evs048

20. RayDA, BatzerMA (2005) Tracking Alu evolution in New World primates. BMC Evol Biol 5: 51 doi:10.1186/1471-2148-5-51

21. BrittenRJ, BaronWF, StoutDB, DavidsonEH (1988) Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci 85: 4770–4774.

22. JurkaJ, MilosavljevicA (1991) Reconstruction and analysis of human Alu genes. J Mol Evol 32: 105–121.

23. Hubley R, Siegel A, Smit A (2008) COSEG, version 0.2.1. Available: http://www.repeatmasker.org/COSEGDownload.html. Accessed 3 March 2014.

24. PriceAL, EskinE, PevznerPA (2004) Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res 14: 2245–2252 doi:10.1101/gr.2693004

25. Smit AFA, Hubley R, Green P (2004) RepeatMasker Open-3.0. Available: http://www.repeatmasker.org.

26. Vemulapalli V (2012) Delineating the evolutionary dynamics of mutation and selection University of Colorado Denver.

27. BrittenRJ (1994) Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago. Proc Natl Acad Sci U S A 91: 6148–6150.

28. LiuGE, AlkanC, JiangL, ZhaoS, EichlerEE (2009) Comparative analysis of Alu repeats in primate genomes. Genome Res 19: 876–885 doi:10.1101/gr.083972.108

29. KapitonovV, JurkalJ (1996) The age of Alu subfamilies. J Mol Evol 42: 59–65 doi:10.1007/BF00163212

30. MarchaniEE, XingJ, WitherspoonDJ, JordeLB, RogersAR (2009) Estimating the age of retrotransposon subfamilies using maximum likelihood. Genomics 94: 78–82 doi:10.1016/j.ygeno.2009.04.002

31. JurkaJ, KapitonovVV, PavlicekA, KlonowskiP, KohanyO, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462–467 doi:10.1159/000084979

32. BlankenbergD, TaylorJ, NekrutenkoA (2011) Making whole genome multiple alignments usable for biologists. Bioinformatics 27: 2426–2428 doi:10.1093/bioinformatics/btr398

33. GuW, CastoeTA, HedgesDJ, BatzerMA, PollockDD (2008) Identification of repeat structure in large genomes using repeat probability clouds. Anal Biochem 380: 77–83 doi:10.1016/j.ab.2008.05.015

34. HastingsWK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97–109 doi:10.1093/biomet/57.1.97