Advertisement

Genes & Genomics

, Volume 41, Issue 7, pp 831–837 | Cite as

A comprehensive analysis of the Baboon-specific full-length LINE-1 retrotransposons

  • Wooseok Lee
  • Minhoon Choi
  • Songmi Kim
  • Wanxiangfu Tang
  • Dong Hee Kim
  • Heui-Soo Kim
  • Ping Liang
  • Kyudong HanEmail author
Research Article
  • 67 Downloads

Abstract

Background

Long interspersed elements-1 (LINE-1s or L1s) and Alu elements are most successful retrotransposons that have generated genetic diversity and genomic fluidity in the primate genome. They account for ~ 27.7% of the primate genome. Interestingly, a previous study has shown that the retrotransposition rate of Alu elements is nine times higher in baboons than in humans.

Objective

The expansion of Alu copies could be dependent on the activity of L1-encoded proteins. Thus, we aimed to investigate full-length baboon-specific L1s and characterize structurally and functionally intact baboon-specific L1s (ORF1p/ORF2p and ORF2p only) that could induce trans-mobilization of Alu elements in the baboon genome.

Results

A total of 673 baboon-specific L1 candidates (> 4 kb) were identified through the comparative genomic analysis. Applying the baboon-specific correction value obtained from the experimental validation, it demonstrated that approximately 446 baboon-specific L1s (> 4 kb) were present in the baboon reference genome (papAnu2). In addition, we observed phylogenetic relationship of the baboon-specific L1s through the neighbor-joining method and they diverged from the L1PA6 consensus sequence. Finally, we identified 36 full-length baboon-specific L1s that were intact both ORF1p and ORF2p.

Conclusion

The number of baboon-specific full-length L1s is fewer than the number of human-specific full-length L1s. Therefore, there is possibility that the “L1 master gene” or “L1 source gene” is more abundant in the baboon genome, or that in trans retrotransposition activity of baboon-specific L1s is relatively stronger than in the other genomes.

Keywords

Baboon Transposable element LINE-1 Baboon-specific 

Notes

Compliance with ethical standards

Conflict of interest

Wooseok Lee, Minhoon Choi, Songmi Kim, Wanxiangfu Tang, Dong Hee Kim, Heui-Soo Kim, Ping Liang and Kyudong Han declare that we have no conflict of interest.

Ethical approval

This study was conducted in accordance with South Korea laws and the guidelines of the Kyoto University’s Primate Research Institute.

Supplementary material

13258_2019_794_MOESM1_ESM.pdf (22 kb)
Supplementary material 1 Supplementary Figure 1. Phylogenetic tree of 167 baboon-specific L1s (>5 kb) and L1PA subfamilies. The neighbor-joining tree was constructed by using 167 baboon-specific L1 sequences (>5 kb) and L1PA consensus sequences. Bootstrap value (> 70%) based on 1000 replications are shown (PDF 21 KB)
13258_2019_794_MOESM2_ESM.xlsx (17 kb)
Supplementary material 2 (XLSX 16 KB)

References

  1. Clements AP, Singer MF (1998) The human LINE-1 reverse transcriptase:effect of deletions outside the common reverse transcriptase domain. Nucleic Acids Res 26:3528–3535CrossRefGoogle Scholar
  2. Dewannieux M, Esnault C, Heidmann T (2003) LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35:41–48CrossRefGoogle Scholar
  3. Ejima Y, Yang L (2003) Trans mobilization of genomic DNA as a mechanism for retrotransposon-mediated exon shuffling. Hum Mol Genet 12:1321–1328CrossRefGoogle Scholar
  4. Garcia-Perez JL, Doucet AJ, Bucheton A, Moran JV, Gilbert N (2007) Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase. Genome Res 17:602–611CrossRefGoogle Scholar
  5. Glazko GV, Nei M (2003) Estimation of divergence times for major lineages of primate species. Mol Biol Evol 20:424–434CrossRefGoogle Scholar
  6. Han JS, Boeke JD (2004) A highly active synthetic mammalian retrotransposon. Nature 429:314–318CrossRefGoogle Scholar
  7. Han K, Xing J, Wang H, Hedges DJ, Garber RK, Cordaux R, Batzer MA (2005) Under the genomic radar: the stealth model of Alu amplification. Genome Res 15:655–664CrossRefGoogle Scholar
  8. Han K, Konkel MK, Xing J, Wang H, Lee J, Meyer TJ, Huang CT, Sandifer E, Hebert K, Barnes EW et al (2007) Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome. Science 316:238–240CrossRefGoogle Scholar
  9. Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE (2010) Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 141:1253–1261CrossRefGoogle Scholar
  10. Khan H, Smit A, Boissinot S (2006) Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res 16:78–87CrossRefGoogle Scholar
  11. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefGoogle Scholar
  12. Konkel MK, Walker JA, Batzer MA (2010) LINEs and SINEs of primate evolution. Evol Anthropol 19:236–249CrossRefGoogle Scholar
  13. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948CrossRefGoogle Scholar
  14. Lee J, Mun S, Meyer TJ, Han K (2012) High levels of sequence diversity in the 5′ UTRs of human-specific L1 elements. Comp Funct Genom 2012:129416Google Scholar
  15. Liu GE, Alkan C, Jiang L, Zhao S, Eichler EE (2009) Comparative analysis of Alu repeats in primate genomes. Genome Res 19:876–885CrossRefGoogle Scholar
  16. Newman TK, Jolly CJ, Rogers J (2004) Mitochondrial phylogeny and systematics of baboons (Papio). Am J Phys Anthropol 124:17–27CrossRefGoogle Scholar
  17. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  18. Schmid CW (1996) Alu: structure, origin, evolution, significance and function of one-tenth of human DNA. Prog Nucleic Acid Res Mol Biol 53:283–319CrossRefGoogle Scholar
  19. Shen MR, Batzer MA, Deininger PL (1991) Evolution of the master Alu gene(s). J Mol Evol 33:311–320CrossRefGoogle Scholar
  20. Smit AF, Toth G, Riggs AD, Jurka J (1995) Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J Mol Biol 246:401–417CrossRefGoogle Scholar
  21. Steely CJ, Baker JN, Walker JA, Loupe CD III, Baboon Genome Analysis C, Batzer MA (2018) Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis. Mob DNA 9:10CrossRefGoogle Scholar
  22. Tang W, Mun S, Joshi A, Han K, Liang P (2018) Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase. DNA Res 25:521–533CrossRefGoogle Scholar
  23. Zinner D, Groeneveld LF, Keller C, Roos C (2009) Mitochondrial phylogeography of baboons (Papio spp.): indication for introgressive hybridization? BMC Evol Biol 9:83CrossRefGoogle Scholar

Copyright information

© The Genetics Society of Korea 2019

Authors and Affiliations

  1. 1.Department of Nanobiomedical Science, BK21 PLUS NBM Global Research Center for Regenerative MedicineDankook UniversityCheonanRepublic of Korea
  2. 2.DKU-Theragen institute for NGS analysis (DTiNa)CheonanRepublic of Korea
  3. 3.Department of Biological SciencesBrock UniversitySt. CatharinesCanada
  4. 4.Department of Anesthesiology and Pain Management, College of MedicineDankook UniversityCheonanRepublic of Korea
  5. 5.Department of Biological Sciences, College of Natural SciencesPusan National UniversityBusanRepublic of Korea

Personalised recommendations