DOI QR코드

DOI QR Code

Novel Discovery of LINE-1 in a Korean Individual by a Target Enrichment Method

  • Shin, Wonseok (Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University) ;
  • Mun, Seyoung (Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University) ;
  • Kim, Junse (Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University) ;
  • Lee, Wooseok (Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University) ;
  • Park, Dong-Guk (Department of Surgery, Dankook University College of Medicine) ;
  • Choi, Seungkyu (Department of Pathology, Dankook University College of Medicine) ;
  • Lee, Tae Yoon (Department of Technology Education and Department of Biomedical Engineering, Chungnam National University) ;
  • Cha, Seunghee (Department of Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry) ;
  • Han, Kyudong (Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University)
  • Received : 2018.08.17
  • Accepted : 2018.10.26
  • Published : 2019.01.31

Abstract

Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.

E1BJB7_2019_v42n1_87_f0001.png 이미지

Fig. 1. The workflow of L1Hs-targeted enrichment library preparation.

E1BJB7_2019_v42n1_87_f0002.png 이미지

Fig. 2. The design of the probe specific for the L1Hs-target sequence.

E1BJB7_2019_v42n1_87_f0003.png 이미지

Fig. 3. NGS Data analysis.

E1BJB7_2019_v42n1_87_f0004.png 이미지

Fig. 4. Comparison of the L1 composition on the genes of non-reference L1Hs insertion and on the human genes.

Table 1. Summary of the high-throughput sequencing data

E1BJB7_2019_v42n1_87_t0001.png 이미지

Table 2. Summary of non-reference L1Hs elements in the KPGP9 genome

E1BJB7_2019_v42n1_87_t0002.png 이미지

Acknowledgement

Supported by : National Research Foundation of Korea (NRF)

References

  1. Ayarpadikannan, S., and Kim, H.S. (2014). The impact of transposable elements in genome evolution and genetic instability and their implications in various diseases. Genomics Inform. 12, 98-104. https://doi.org/10.5808/GI.2014.12.3.98
  2. Badge, R.M., Alisch, R.S., and Moran, J.V. (2003). ATLAS: a system to selectively identify human-specific L1 insertions. Am. J. Hum. Genet. 72, 823-838. https://doi.org/10.1086/373939
  3. Beck, C.R., Collier, P., Macfarlane, C., Malig, M., Kidd, J.M., Eichler, E.E., Badge, R.M., and Moran, J.V. (2010). LINE-1 retrotransposition activity in human genomes. Cell 141, 1159-1170. https://doi.org/10.1016/j.cell.2010.05.021
  4. Beck, C.R., Garcia-Perez, J.L., Badge, R.M., and Moran, J.V. (2011). LINE-1 elements in structural variation and disease. Annu. Rev. Genomics. Hum. Genet. 12, 187-215. https://doi.org/10.1146/annurev-genom-082509-141802
  5. Bennett, E.A., Keller, H., Mills, R.E., Schmidt, S., Moran, J.V., Weichenrieder, O., and Devine, S.E. (2008). Active Alu retrotransposons in the human genome. Genome. Res. 18, 1875-1883. https://doi.org/10.1101/gr.081737.108
  6. Boissinot, S., Chevret, P., and Furano, A.V. (2000). L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 17, 915-928. https://doi.org/10.1093/oxfordjournals.molbev.a026372
  7. Boissinot, S., Entezam, A., Young, L., Munson, P.J., and Furano, A.V. (2004). The insertional history of an active family of L1 retrotransposons in humans. Genome Res. 14, 1221-1231. https://doi.org/10.1101/gr.2326704
  8. Brouha, B., Schustak, J., Badge, R.M., Lutz-Prigge, S., Farley, A.H., Moran, J.V., and Kazazian, H.H., Jr. (2003). Hot L1s account for the bulk of retrotransposition in the human population. Proc. Natl. Acad. Sci. USA 100, 5280-5285. https://doi.org/10.1073/pnas.0831042100
  9. Collier, L.S., Carlson, C.M., Ravimohan, S., Dupuy, A.J., and Largaespada, D.A. (2005). Cancer gene discovery in solid tumours using transposon-based somatic mutagenesis in the mouse. Nature 436, 272-276. https://doi.org/10.1038/nature03681
  10. Cordaux, R., and Batzer, M.A. (2009). The impact of retrotransposons on human genome evolution. Nat. Rev. Genet. 10, 691-703. https://doi.org/10.1038/nrg2640
  11. Dewannieux, M., Esnault, C., and Heidmann, T. (2003). LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35, 41-48. https://doi.org/10.1038/ng1223
  12. Ewing, A.D. (2015). Transposable element detection from whole genome sequence data. Mob. DNA 6, 24. https://doi.org/10.1186/s13100-015-0055-3
  13. Ewing, A.D., and Kazazian, H.H., Jr. (2010). High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res. 20, 1262-1270. https://doi.org/10.1101/gr.106419.110
  14. Fanning, T., and Singer, M. (1987). The LINE-1 DNA sequences in four mammalian orders predict proteins that conserve homologies to retrovirus proteins. Nucleic Acids Res. 15, 2251-2260. https://doi.org/10.1093/nar/15.5.2251
  15. Iskow, R.C., McCabe, M.T., Mills, R.E., Torene, S., Pittard, W.S., Neuwald, A.F., Van Meir, E.G., Vertino, P.M., and Devine, S.E. (2010). Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 141, 1253-1261. https://doi.org/10.1016/j.cell.2010.05.020
  16. Kenny, E.M., Cormican, P., Gilks, W.P., Gates, A.S., O'Dushlaine, C.T., Pinto, C., Corvin, A.P., Gill, M., and Morris, D.W. (2011). Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection. DNA Res. 18, 31-38. https://doi.org/10.1093/dnares/dsq029
  17. Konkel, M.K., Wang, J., Liang, P., and Batzer, M.A. (2007). Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies. Gene 390, 28-38. https://doi.org/10.1016/j.gene.2006.07.040
  18. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921. https://doi.org/10.1038/35057062
  19. Lun, A.T., and Smyth, G.K. (2016). csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows. Nucleic Acids Res. 44, e45. https://doi.org/10.1093/nar/gkv1191
  20. Lutz, S.M., Vincent, B.J., Kazazian, H.H., Jr., Batzer, M.A., and Moran, J.V. (2003). Allelic heterogeneity in LINE-1 retrotransposition activity. Am. J. Hum. Genet. 73, 1431-1437. https://doi.org/10.1086/379744
  21. Myers, J.S., Vincent, B.J., Udall, H., Watkins, W.S., Morrish, T.A., Kilroy, G.E., Swergold, G.D., Henke, J., Henke, L., Moran, J.V., et al. (2002). A comprehensive analysis of recently integrated human Ta L1 elements. Am. J. Hum. Genet. 71, 312-326. https://doi.org/10.1086/341718
  22. O'Donnell, K.A., and Burns, K.H. (2010). Mobilizing diversity: transposable element insertions in genetic variation and disease. Mob. DNA 1, 21. https://doi.org/10.1186/1759-8753-1-21
  23. Ovchinnikov, I., Rubin, A., and Swergold, G.D. (2002). Tracing the LINEs of human evolution. Proc. Natl. Acad. Sci. USA 99, 10522-10527. https://doi.org/10.1073/pnas.152346799
  24. Ovchinnikov, I., Troxel, A.B., and Swergold, G.D. (2001). Genomic characterization of recent human LINE-1 insertions: evidence supporting random insertion. Genome Res. 11, 2050-2058. https://doi.org/10.1101/gr.194701
  25. Park, S.J., Kim, Y.H., Lee, S.R., Choe, S.H., Kim, M.J., Kim, S.U., Kim, J.S., Sim, B.W., Song, B.S., Jeong, K.J., et al. (2015). Gain of a new exon by a lineage-specific Alu element-Integration event in the BCS1L gene during primate evolution. Mol. Cells. 38, 950-958. https://doi.org/10.14348/molcells.2015.0121
  26. Philippe, C., Vargas-Landin, D.B., Doucet, A.J., van Essen, D., Vera-Otarola, J., Kuciak, M., Corbin, A., Nigumann, P., and Cristofari, G. (2016). Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci. Elife. 5.
  27. Schrader, L., and Schmitz, J. (2018). The impact of transposable elements in adaptive evolution. Mol. Ecol. [In press] Available at: https://doi.org/110.1111/mec.14794.
  28. Seleme, M.C., Vetter, M.R., Cordaux, R., Bastone, L., Batzer, M.A., and Kazazian, H.H., Jr. (2006). Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity. Proc. Natl. Acad. Sci. USA 103, 6611-6616. https://doi.org/10.1073/pnas.0601324103
  29. Sellis, D., Provata, A., and Almirantis, Y. (2007). Alu and LINE1 distributions in the human chromosomes: evidence of global genomic organization expressed in the form of power laws. Mol. Biol. Evol. 24, 2385-2399. https://doi.org/10.1093/molbev/msm181
  30. Smith, A.M., Heisler, L.E., Mellor, J., Kaper, F., Thompson, M.J., Chee, M., Roth, F.P., Giaever, G., and Nislow, C. (2009). Quantitative phenotyping via deep barcode sequencing. Genome Res. 19, 1836-1842. https://doi.org/10.1101/gr.093955.109
  31. Sotero-Caio, C.G., Platt, R.N., 2nd, Suh, A., and Ray, D.A. (2017). Evolution and diversity of transposable elements in vertebrate genomes. Genome Biol. Evol. 9, 161-177. https://doi.org/10.1093/gbe/evw264
  32. Steinhauser, S., Kurzawa, N., Eils, R., and Herrmann, C. (2016). A comprehensive comparison of tools for differential ChIP-seq analysis. Brief Bioinform. 17, 953-966. https://doi.org/10.1093/bib/bbv110
  33. Streva, V.A., Jordan, V.E., Linker, S., Hedges, D.J., Batzer, M.A., and Deininger, P.L. (2015). Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals. BMC Genomics. 16, 220. https://doi.org/10.1186/s12864-015-1374-y
  34. Strino, F., and Lappe, M. (2016). Identifying peaks in *-seq data using shape information. BMC Bioinformatics 17 Suppl 5, 206. https://doi.org/10.1186/s12859-016-1042-5
  35. Tripathi, S., Pohl, M.O., Zhou, Y., Rodriguez-Frandsen, A., Wang, G., Stein, D.A., Moulton, H.M., DeJesus, P., Che, J., Mulder, L.C., et al. (2015). Meta- and orthogonal integration of influenza "OMICs" data defines a role for UBR4 in virus budding. Cell Host Microbe. 18, 723-735. https://doi.org/10.1016/j.chom.2015.11.002
  36. Valencia, C.A., Rhodenizer, D., Bhide, S., Chin, E., Littlejohn, M.R., Keong, L.M., Rutkowski, A., Bonnemann, C., and Hegde, M. (2012). Assessment of target enrichment platforms using massively parallel sequencing for the mutation detection for congenital muscular dystrophy. J. Mol. Diagn. 14, 233-246. https://doi.org/10.1016/j.jmoldx.2012.01.009
  37. Van den Broeck, D., Maes, T., Sauer, M., Zethof, J., De Keukeleire, P., D'Hauw, M., Van Montagu, M., and Gerats, T. (1998). Transposon Display identifies individual transposable elements in high copy number lines. Plant J. 13, 121-129. https://doi.org/10.1046/j.1365-313X.1998.00004.x
  38. Wang, L., Norris, E.T., and Jordan, I.K. (2017). Human retrotransposon insertion polymorphisms are associated with health and disease via gene regulatory phenotypes. Front Microbiol. 8, 1418. https://doi.org/10.3389/fmicb.2017.01418
  39. Witherspoon, D.J., Xing, J., Zhang, Y., Watkins, W.S., Batzer, M.A., and Jorde, L.B. (2010). Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC Genomics. 11, 410. https://doi.org/10.1186/1471-2164-11-410