Role of Retrotransposon Activity in Neurodegeneration and Alzheimer's Disease - Publication List

  1. Gnanakkan VP, Jaffe AE, Dai L, Fu J, Wheelan SJ, Levitsky HI, Boeke JD, Burns KH. TE-array--a high throughput tool to study transposon transcription. BMC Genomics. 2013 Dec 10;14:869. doi: 10.1186/1471-2164-14-869. PubMed PMID: 24325565; PubMed Central PMCID: PMC3878892.

  2. Belfort M, Marraffini L, Macfarlan T, Boeke J, Slotkin K, Malik H, Maquat L.  2014. Mobile DNA: an evolving field. Mob DNA. 5:16. PubMed PMID: 24904692; PubMed Central PMCID: PMC4046146.

  3. Dai L, LaCava J, Taylor MS, Boeke JD. 2014 Expression and detection of LINE-1 ORF-encoded proteins. Mob Genet Elements. 4:e29319. eCollection 2014. PMID: 25054082; PMCID: PMC4091050.

  4. Gorbunova V, Boeke JD, Helfand SL, Sedivy JM. Human Genomics. Sleeping dogs of the genome. Science. 2014 346:1187-8. PMCID: PMC4312280.

  5. Taylor MS, Lacava J, Mita P, Molloy KR, Huang CR, Li D, Adney EM, Jiang H, Burns KH, Chait BT, Rout MP, Boeke JD, Dai L. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell 2013 Nov 21;155(5):1034-48. doi: 10.1016/j.cell.2013.10.021.

  6. Terasaki N, Goodier JL, Cheung LE, Wang YJ, Kajikawa M, Kazazian HH Jr, Okada N. In vitro screening for compounds that enhance human L1 mobilization. PLoS One 2013 Sep 11;8(9):e74629.

  7. Zhao K, Du J, Han X, Goodier JL, Li P, Zhou X, Wei W, Evans SL, Li L, Zhang W, Cheung LE, Wang G, Kazazian HH Jr, and Yu XF. Modulation of LINE-1 and Alu/SVA retrotransposition by Aicardi-Goutières syndrome-related SAMHD1. Cell Rep. 2013 Sep 26; 1108-15.

  8. McLaughlin RN Jr, Young JM, Yang L, Neme R, Wichman HA, Malik HS. Positive selection and multiple losses of the LINE-1-derived L1TD1 gene in mammals suggest a dual role in genome defense and pluripotency. PLoS Genet. 2014 Sep 11;10(9):e1004531. doi: 10.1371/journal.pgen.1004531. PMID: 25211013; PMCID: PMC4161310.

  9. Rodić N, Sharma R, Sharma R, Zampella J, Dai L, Taylor MS, Hruban RH, Iacobuzio-Donahue CA, Maitra A, Torbenson MS, Goggins M, Shih IeM, Duffield AS, Montgomery EA, Gabrielson E, Netto GJ, Lotan TL, De Marzo AM, Westra W, Binder ZA, Orr BA, Gallia GL, Eberhart CG, Boeke JD, Harris CR, Burns KH. 2014 Long interspersed element-1 protein expression is a hallmark of many human cancers. Am J Pathol. 184:1280-6. PMCID: PMC4005969.

  10. Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA. Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinformatics. 2014 Jun 1;30(11):1514-21. PubMed PMID: 24501098; PubMed Central PMCID: PMC4029030.

  11. Daugherty MD, Young JM, Kerns JA, Malik HS. Rapid evolution of PARP genes suggests a broad role for ADP-ribosylation in host-virus conflicts. 2014 PLoS Genet.

    May 29;10(5):e1004403. doi: 10.1371/journal.pgen.1004403. eCollection 2014. PubMed PMID: 24875882; PubMed Central PMCID: PMC4038475.

  12. Shimizu A, Nakatani Y, Nakamura T, Jinno-Oue A, Ishikawa O, Boeke JD, Takeuchi Y, Hoshino H. Characterisation of cytoplasmic DNA complementary to non-retroviral RNA viruses in human cells. Sci Rep. 2014 May 30;4:5074. doi: 10.1038/srep05074.  PubMed PMID: 24875540; PubMed Central PMCID: PMC4038843.

  13. Boeke JD, Fenyö D. Much Ado about Zero. Cell. 2015 Oct 22;163(3):534-5. PubMed PMID: 26496595.

  14. Rodić N, Steranka JP, Makohon-Moore A, Moyer A, Shen P, Sharma R, Kohutek ZA, Huang CR, Ahn D, Mita P, Taylor MS, Barker NJ, Hruban RH, Iacobuzio-Donahue CA, Boeke JD, Burns KH. Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma. Nat Med. 2015; Sep;21(9): 1060-4. PubMed PMID: 26259033.

  15. Doucet-O'Hare TT, Rodić N, Sharma R, Darbari I, Abril G, Choi JA, Young Ahn J, Cheng Y, Anders RA, Burns KH, Meltzer SJ, Kazazian HH Jr. LINE-1 expression and retrotransposition in Barrett's esophagus and esophageal carcinoma. Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):E4894-900. PubMed PMID: 26283398; PubMed Central PMCID: PMC4568228.

  16. Ewing AD, Gacita A, Wood LD Ma F, Xing D, Kim M-S, Manda SS, Gabriela Abril  G, Pereira G, Makohon-Moore A, Looijenga LHJ, Gillis AJM, Hruban  RH, Anders RA, Romans KE,Pandey A, Iacobuzio-Donahue CA, Vogelstein B, Kinzler KW, Kazazian HH Jr.*, Solyom S*. 2015 Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution. Genome Research, 25(10):1536-45.

  17. LaCava, J., Molloy, K. R., Taylor, M. S., Domanski, M., Chait, B. T., & Rout, M. P. 2015. Affinity proteomics to study endogenous protein complexes: Pointers, pitfalls, preferences and perspectives. BioTechniques, 58(3), 103–119.

  18. Grandi, F.C., Rosser, J.M., Newkirk, S.J., Yin, J., Jiang, X., Xing, Z., Whitmore, L., Bashir, S., Ivics, Z., Izsvák, Z., Ye, P., Yu, Y.E. & An, W. Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites. Genome Research. 2015. 25: 1135-1146.

  19. Mitchell PS, Young JM, Emerman M, Malik HS. Evolutionary Analyses Suggest a Function of MxB Immunity Proteins Beyond Lentivirus Restriction. PLoS Pathog. 2015 Dec 10;11(12):e1005304. PubMed PMID: 26658285; PubMed Central PMCID: PMC4687636.

  20. McLaughlin RN Jr, Malik HS. LINE-1 Retroelements Get ZAPped! PLoS Genet. 2015. Jul 16;11(7):e1005364. doi: 10.1371/journal.pgen.1005364. eCollection 2015 Jul.

    PubMed PMID: 26182081; PubMed Central PMCID: PMC4504689.

  21. Ewing AD, Gacita A, Wood LD Ma F, Xing D, Kim M-S, Manda SS, Gabriela Abril  G, Pereira G, Makohon-Moore A, Looijenga LHJ, Gillis AJM, Hruban  RH, Anders RA, Romans KE,Pandey A, Iacobuzio-Donahue CA, Vogelstein B, Kinzler KW, Kazazian HH Jr.*, Solyom S*. Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution. Genome Research, 2015 Oct;25 (10):1536-45. PMCID: PMC4579339 (*corresponding authors).

  22. Yang K, Stracquadanio G, Luo J, Boeke JD, Bader JS. BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. Bioinformatics. 2015 Nov 14. pii: btv664. PMCID: PMC4803390.

  23. McLaughlin RN Jr, Gable JT, Wittkopp CJ, Emerman M, Malik HS. Conservation and Innovation of APOBEC3A Restriction Functions during Primate Evolution. Mol Biol Evol. 2016 Aug;33(8):1889-901. doi: 10.1093/molbev/msw070. Epub 2016 Apr 6. PMID: 27189538; PMCID: PMC5010000.

  24. Doucet-O'Hare TT, Sharma R, Rodić N, Anders RA, Burns KH, Kazazian HH Jr. Somatically Acquired LINE-1 Insertions in Normal Esophagus Undergo Clonal Expansion in Esophageal Squamous Cell Carcinoma. Hum Mutat. 2016 Sep;37(9):942-54. doi: 10.1002/humu.23027. Epub 2016 Jul 13. PMID: 27319353; PMCID: PMC5548391.

  25. Reema Sharma, Nemanja Rodić, Kathleen H. Burns, Martin S. Taylor. 2016 Immuno-Detection of Human LINE-1 expression. In "Methods in Molecular Biology; Retrotransposons and Transposons", Jose Luis García Pérez, Ed., Humana Press.

  26. Martin S. Taylor, John LaCava, Lixin Dai, Kathleen H. Burns, Michael P. Rout, and Jef D. Boeke. 2016 Characterization of L1-RNPs. In "Methods in Molecular Biology; Retrotransposons and Transposons", Jose Luis García Pérez, Ed., Humana Press.

  27. Doucet TT, Kazazian HHK Jr. 2016 Long interspersed element sequencing (L1-seq): a method to identify somatic LINE-1 insertions in the human genome.  In "Methods in Molecular Biology; Retrotransposons and Transposons", Jose Luis García Pérez, Ed., Humana Press.

  28. Prabhat K. Mandal, Haig H. Kazazian Jr. 2016 Purification of L1-ribonucleoprotein particles (L1-RNPs) from cultured human cells. In "Methods in Molecular Biology; Retrotransposons and Transposons", Jose Luis García Pérez, Ed., Humana Press.

  29. Achanta P, Steranka JP, Tang Z, Rodić N, Sharma R, Yang WR, Ma S, Grivainis M, Huang CRL, Schneider AM, Gallia GL, Riggins GJ, Quinones-Hinojosa A, Fenyö D, Boeke JD, Burns KH. Somatic retrotransposition is infrequent in glioblastomas. Mob DNA. 2016 Nov 11;7:22. doi: 10.1186/s13100-016-0077-5. PMID: 27843500; PMCID: PMC5105304.

  30. Zampella JG, Rodić N, Yang WR, Huang CR, Welch J, Gnanakkan VP, Cornish TC, Boeke JD, Burns KH. A map of mobile DNA insertions in the NCI-60 human cancer cell panel. Mob DNA. 2016 Oct 31;7:20. doi: 10.1186/s13100-016-0078-4. PMID: 27807467; PMCID: PMC5087121.

  31. Newkirk SJ, Lee S, Grandi FC, Gaysinskaya V, Rosser JM, Vanden Berg N, Hogarth CA, Marchetto MCN, Muotri AR, Griswold MD, Ye P, Bortvin A, Gage FH, Boeke JD, An W. Intact piRNA pathway prevents L1 mobilization in male meiosis. Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):E5635-E5644. doi: 10.1073/pnas.1701069114. Epub 2017 Jun 19. PMID: 28630288; PMCID: PMC5514719.

  32. Tang Z, Steranka JP, Ma S, Grivainis M, Rodić N, Huang CR, Shih IM, Wang TL, Boeke JD, Fenyö D, Burns KH. Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer. Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):E733-E740. doi: 10.1073/pnas.1619797114. Epub 2017 Jan 17. PMID: 28096347; PMCID: PMC5293032.

  33. Mita P, Wudzinska A, Sun X, Andrade J, Nayak S, Kahler DJ, Badri S, LaCava J, Ueberheide B, Yun CY, Fenyö D, Boeke JD. LINE-1 protein localization and functional dynamics during the cell cycle. Elife. 2018 Jan 8;7:e30058. doi: 10.7554/eLife.30058. PMID: 29309036; PMCID: PMC5821460.

  34. Taylor MS, Altukhov I, Molloy KR, Mita P, Jiang H, Adney EM, Wudzinska A, Badri S, Ischenko D, Eng G, Burns KH, Fenyö D, Chait BT, Alexeev D, Rout MP, Boeke JD, LaCava J. Dissection of affinity captured LINE-1 macromolecular complexes. Elife. 2018 Jan 8;7:e30094. doi: 10.7554/eLife.30094. PMID: 29309035; PMCID: PMC5821459.

  35. Mita P, Boeke JD. Cycling to Maintain and Improve Fitness: Line-1 Modes of Nuclear Entrance and Retrotransposition. SLAS Discov. 2018 Jul;23(6):491-494. doi: 10.1177/2472555218767842. Epub 2018 May 3. PMID: 29724131.

  36. Sun X, Wang X, Tang Z, Grivainis M, Kahler D, Yun C, Mita P, Fenyö D, Boeke JD. Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression. Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):E5526-E5535. doi: 10.1073/pnas.1722565115. Epub 2018 May 25. PMID: 29802231; PMCID: PMC6004460.

  37. Steranka JP, Tang Z, Grivainis M, Huang CRL, Payer LM, Rego FOR, Miller TLA, Galante PAF, Ramaswami S, Heguy A, Fenyö D, Boeke JD, Burns KH. Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome. Mob DNA. 2019 Mar 8;10:8. doi: 10.1186/s13100-019-0148-5. PMID: 30899333; PMCID: PMC6407172.

  38. Adney EM, Ochmann MT, Sil S, Truong DM, Mita P, Wang X, Kahler DJ, Fenyö D, Holt LJ, Boeke JD. Comprehensive Scanning Mutagenesis of Human Retrotransposon LINE-1 Identifies Motifs Essential for Function. Genetics. 2019 Dec;213(4):1401-1414. doi: 10.1534/genetics.119.302601. Epub 2019 Oct 30. PMID: 31666291; PMCID: PMC6893370.

  39. Ardeljan D, Steranka JP, Liu C, Li Z, Taylor MS, Payer LM, Gorbounov M, Sarnecki JS, Deshpande V, Hruban RH, Boeke JD, Fenyö D, Wu PH, Smogorzewska A, Holland AJ, Burns KH. Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication. Nat Struct Mol Biol. 2020 Feb;27(2):168-178. doi: 10.1038/s41594-020-0372-1. Epub 2020 Feb 10. PMID: 32042151; PMCID: PMC7080318.

  40. Mita P, Sun X, Fenyö D, Kahler DJ, Li D, Agmon N, Wudzinska A, Keegan S, Bader JS, Yun C, Boeke JD. BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells. Nat Struct Mol Biol. 2020 Feb;27(2):179-191. doi: 10.1038/s41594-020-0374-z. Epub 2020 Feb 10. PMID: 32042152; PMCID: PMC7082080.