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Library Construction for High-Throughput Mobile Element Identification and Genotyping

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Population Epigenetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1589))

Abstract

Mobile genetic elements are discrete DNA elements that can move around and copy themselves in a genome. As a ubiquitous component of the genome, mobile elements contribute to both genetic and epigenetic variation. Therefore, it is important to determine the genome-wide distribution of mobile elements. Here we present a targeted high-throughput sequencing protocol called Mobile Element Scanning (ME-Scan) for genome-wide mobile element detection. We will describe oligonucleotides design, sequencing library construction, and computational analysis for the ME-Scan protocol.

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References

  1. de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD (2011) Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet 7(12), e1002384. doi:10.1371/journal.pgen.1002384

    Article  PubMed  PubMed Central  Google Scholar 

  2. Pace JK II, Feschotte C (2007) The evolutionary history of human DNA transposons: evidence for intense activity in the primate lineage. Genome Res 17(4):422–432. doi:10.1101/gr.5826307

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Ostertag EM, Kazazian HH Jr (2001) Biology of mammalian L1 retrotransposons. Annu Rev Genet 35:501–538

    Article  CAS  PubMed  Google Scholar 

  4. Dewannieux M, Esnault C, Heidmann T (2003) LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35(1):41–48

    Article  CAS  PubMed  Google Scholar 

  5. Hancks DC, Goodier JL, Mandal PK, Cheung LE, Kazazian HH Jr (2011) Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum Mol Genet 20(17):3386–3400. doi:10.1093/hmg/ddr245

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Raiz J, Damert A, Chira S, Held U, Klawitter S, Hamdorf M, Lower J, Stratling WH, Lower R, Schumann GG (2012) The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery. Nucleic Acids Res 40(4):1666–1683. doi:10.1093/nar/gkr863

    Article  CAS  PubMed  Google Scholar 

  7. Burns KH, Boeke JD (2012) Human transposon tectonics. Cell 149(4):740–752. doi:10.1016/j.cell.2012.04.019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, Jorde LB (2009) Mobile elements create structural variation: analysis of a complete human genome. Genome Res 19(9):1516–1526. doi:10.1101/gr.091827.109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Ichiyanagi K (2013) Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs. Genes Genet Syst 88(1):19–29

    Article  CAS  PubMed  Google Scholar 

  10. Cowley M, Oakey RJ (2013) Transposable elements re-wire and fine-tune the transcriptome. PLoS Genet 9(1), e1003234. doi:10.1371/journal.pgen.1003234

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Piriyapongsa J, Marino-Ramirez L, Jordan IK (2007) Origin and evolution of human microRNAs from transposable elements. Genetics 176(2):1323–1337. doi:10.1534/genetics.107.072553

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Rouget C, Papin C, Boureux A, Meunier AC, Franco B, Robine N, Lai EC, Pelisson A, Simonelig M (2010) Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467(7319):1128–1132. doi:10.1038/nature09465

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Wilson MH, Coates CJ, George AL Jr (2007) PiggyBac transposon-mediated gene transfer in human cells. Mol Ther 15(1):139–145. doi:10.1038/sj.mt.6300028

    Article  CAS  PubMed  Google Scholar 

  14. Mann MB, Jenkins NA, Copeland NG, Mann KM (2013) Sleeping Beauty mutagenesis: exploiting forward genetic screens for cancer gene discovery. Curr Opin Genet Dev 24:16–22. doi:10.1016/j.gde.2013.11.004

    Article  PubMed  Google Scholar 

  15. Van den Broeck D, Maes T, Sauer M, Zethof J, De Keukeleire P, D’Hauw M, Van Montagu M, Gerats T (1998) Transposon display identifies individual transposable elements in high copy number lines. Plant J 13(1):121–129. doi:10.1046/j.1365-313X.1998.00004.x

    PubMed  Google Scholar 

  16. Xing J, Wang H, Han K, Ray DA, Huang CH, Chemnick LG, Stewart CB, Disotell TR, Ryder OA, Batzer MA (2005) A mobile element based phylogeny of Old World monkeys. Mol Phylogenet Evol 37(3):872–880. doi:10.1016/j.ympev.2005.04.015

    Article  CAS  PubMed  Google Scholar 

  17. Xing J, Witherspoon DJ, Jorde LB (2013) Mobile element biology: new possibilities with high-throughput sequencing. Trends Genet 29(5):280–289. doi:10.1016/j.tig.2012.12.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Ray DA, Batzer MA (2011) Reading TE leaves: new approaches to the identification of transposable element insertions. Genome Res 21(6):813–820. doi:10.1101/gr.110528.110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Stewart C, Kural D, Stromberg MP, Walker JA, Konkel MK, Stutz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT, Genomes P (2011) A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet 7(8), e1002236. doi:10.1371/journal.pgen.1002236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Witherspoon DJ, Xing J, Zhang Y, Watkins WS, Batzer MA, Jorde LB (2010) Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC Genomics 11:410. doi:10.1186/1471-2164-11-410

    Article  PubMed  PubMed Central  Google Scholar 

  21. Witherspoon DJ, Zhang Y, Xing J, Watkins WS, Ha H, Batzer MA, Jorde LB (2013) Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations. Genome Res 23(7):1170–1181. doi:10.1101/gr.148973.112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760. doi:10.1093/bioinformatics/btp324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT (2014) MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One 9(3), e90581. doi:10.1371/journal.pone.0090581

    Article  PubMed  PubMed Central  Google Scholar 

  24. Smit AF, Hubley R, Green P (1996-2010) RepeatMasker Open-3.0. http://www.repeatmasker.org.

  25. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    Article  CAS  PubMed  Google Scholar 

  26. Ewing AD, Kazazian HH Jr (2010) High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res 20(9):1262–1270. doi:10.1101/gr.106419.110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. 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(7):1253–1261. doi:10.1016/j.cell.2010.05.020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, Badge RM, Moran JV (2010) LINE-1 retrotransposition activity in human genomes. Cell 141(7):1159–1170. doi:10.1016/j.cell.2010.05.021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Huang CR, Schneider AM, Lu Y, Niranjan T, Shen P, Robinson MA, Steranka JP, Valle D, Civin CI, Wang T, Wheelan SJ, Ji H, Boeke JD, Burns KH (2010) Mobile interspersed repeats are major structural variants in the human genome. Cell 141(7):1171–1182. doi:10.1016/j.cell.2010.05.026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC (2010) Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 26(12):i350–i357. doi:10.1093/bioinformatics/btq216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Wang J, Song L, Grover D, Azrak S, Batzer MA, Liang P (2006) dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. Hum Mutat 27(4):323–329. doi:10.1002/humu.20307

    Article  PubMed  PubMed Central  Google Scholar 

  32. Fisher S, Barry A, Abreu J, Minie B, Nolan J, Delorey TM, Young G, Fennell TJ, Allen A, Ambrogio L, Berlin AM, Blumenstiel B, Cibulskis K, Friedrich D, Johnson R, Juhn F, Reilly B, Shammas R, Stalker J, Sykes SM, Thompson J, Walsh J, Zimmer A, Zwirko Z, Gabriel S, Nicol R, Nusbaum C (2011) A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol 12(1):R1. doi:10.1186/gb-2011-12-1-r1

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgement

The authors declare no competing financial interests. We thank Drs. David Ray and Roy Platt for their valuable comments. This study was supported by grants from the National Institutes of Health (R00HG005846).

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Authors and Affiliations

  1. Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ, USA

    Hongseok Ha, Nan Wang & Jinchuan Xing

  2. Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA

    Hongseok Ha, Nan Wang & Jinchuan Xing

Authors
  1. Hongseok Ha
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  2. Nan Wang
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  3. Jinchuan Xing
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Correspondence to Jinchuan Xing .

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Editors and Affiliations

  1. Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeenshire, United Kingdom

    Paul Haggarty

  2. Rowett Institute of Nutrition and Health, University of Aberdeen , Bucksburn, Aberdeenshire, United Kingdom

    Kristina Harrison

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© 2015 Springer Science+Business Media New York

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Ha, H., Wang, N., Xing, J. (2015). Library Construction for High-Throughput Mobile Element Identification and Genotyping. In: Haggarty, P., Harrison, K. (eds) Population Epigenetics. Methods in Molecular Biology, vol 1589. Humana Press, New York, NY. https://doi.org/10.1007/7651_2015_265

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  • DOI: https://doi.org/10.1007/7651_2015_265

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6901-2

  • Online ISBN: 978-1-4939-6903-6

  • eBook Packages: Springer Protocols

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