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Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules

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Transposable Elements

Abstract

During their proliferation and the host’s concomitant attempts to suppress it, LINE-1 (L1) retrotransposons give rise to a collection of heterogeneous ribonucleoproteins (RNPs); their protein and RNA compositions remain poorly defined. The constituents of L1-associated macromolecules can differ depending on numerous factors, including, for example, position within the L1 life cycle, whether the macromolecule is productive or under suppression, and the cell type within which the proliferation is occurring. This chapter describes techniques that aid the capture and characterization of protein and RNA components of L1 macromolecules from tissues that natively express them. The protocols described have been applied to embryonal carcinoma cell lines that are popular model systems for L1 molecular biology (e.g., N2102Ep, NTERA-2, and PA-1 cells), as well as colorectal cancer tissues. N2102Ep cells are given as the use case for this chapter; the protocols should be applicable to essentially any tissue exhibiting endogenous L1 expression with minor modifications.

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Bibliography

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

    Article  CAS  PubMed  Google Scholar 

  2. Moran JV, Gilbert N (2002) Mammalian LINE-1 retrotransposons and related elements. In: Craig NLC, Cragie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. American Society of Microbiology, Washington, DC, pp 836–869

    Google Scholar 

  3. Beauregard A, Curcio MJ, Belfort M (2008) The take and give between retrotransposable elements and their hosts. Annu Rev Genet 42:587–617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Goodier JL, Kazazian HH (2008) Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 135(1):23–35

    Article  CAS  PubMed  Google Scholar 

  5. Paço A, Adega F, Chaves R (2015) LINE-1 retrotransposons: from “parasite” sequences to functional elements. J Appl Genet 56(1):133–145

    Article  PubMed  Google Scholar 

  6. Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV et al (2003) Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A 100(9):5280–5285

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Yang L, Metzger GA, McLaughlin RN. Characterization of LINE-1 transposons in a human genome at allelic resolution. BioRxiv. 1 Apr 2019

    Google Scholar 

  8. Beck CR, Garcia-Perez JL, Badge RM, Moran JV (2011) LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet 12:187–215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Burns KH, Boeke JD (2012) Human transposon tectonics. Cell 149(4):740–752

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Hancks DC, Kazazian HH (2012) Active human retrotransposons: variation and disease. Curr Opin Genet Dev 22(3):191–203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Denli AM, Narvaiza I, Kerman BE, Pena M, Benner C, Marchetto MCN et al (2015) Primate-specific ORF0 contributes to retrotransposon-mediated diversity. Cell 163(3):583–593

    Article  CAS  PubMed  Google Scholar 

  12. Boeke JD, Fenyo D (2015) Much ado about zero. Cell 163(3):534–535

    Article  CAS  PubMed  Google Scholar 

  13. Khazina E, Weichenrieder O (2018) Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p. elife 7:e34960

    Article  PubMed  PubMed Central  Google Scholar 

  14. Khazina E, Truffault V, Büttner R, Schmidt S, Coles M, Weichenrieder O (2011) Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition. Nat Struct Mol Biol 18(9):1006–1014

    Article  CAS  PubMed  Google Scholar 

  15. Rodić N, Sharma R, Sharma R, Zampella J, Dai L, Taylor MS et al (2014) Long interspersed element-1 protein expression is a hallmark of many human cancers. Am J Pathol 184(5):1280–1286

    Article  PubMed  PubMed Central  Google Scholar 

  16. Ardeljan D, Taylor MS, Ting DT, Burns KH (2017) The human long interspersed element-1 retrotransposon: an emerging biomarker of neoplasia. Clin Chem 63(4):816–822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Callahan KE, Hickman AB, Jones CE, Ghirlando R, Furano AV (2012) Polymerization and nucleic acid-binding properties of human L1 ORF1 protein. Nucleic Acids Res 40(2):813–827

    Article  CAS  PubMed  Google Scholar 

  18. Newton JC, Naik MT, Li GY, Murphy EL, Fawzi NL, Sedivy JM et al (2021) Phase separation of the LINE-1 ORF1 protein is mediated by the N-terminus and coiled-coil domain. Biophys J 120(11):2181–2191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Sil S, Boeke JD, Holt LJ. Condensation of LINE-1 is required for retrotransposition. BioRxiv. 11 Apr 2022

    Google Scholar 

  20. Kolosha VO, Martin SL (2003) High-affinity, non-sequence-specific RNA binding by the open reading frame 1 (ORF1) protein from long interspersed nuclear element 1 (LINE-1). J Biol Chem 278(10):8112–8117

    Article  CAS  PubMed  Google Scholar 

  21. Martin SL, Bushman FD (2001) Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol Cell Biol 21(2):467–475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Martin SL, Cruceanu M, Branciforte D, Wai-Lun Li P, Kwok SC, Hodges RS et al (2005) LINE-1 retrotransposition requires the nucleic acid chaperone activity of the ORF1 protein. J Mol Biol 348(3):549–561

    Article  CAS  PubMed  Google Scholar 

  23. Martin SL, Branciforte D, Keller D, Bain DL (2003) Trimeric structure for an essential protein in L1 retrotransposition. Proc Natl Acad Sci U S A 100(24):13815–13820

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Feng Q, Moran JV, Kazazian HH, Boeke JD (1996) Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87(5):905–916

    Article  CAS  PubMed  Google Scholar 

  25. Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH (1996) High frequency retrotransposition in cultured mammalian cells. Cell 87(5):917–927

    Article  CAS  PubMed  Google Scholar 

  26. Ardeljan D, Wang X, Oghbaie M, Taylor MS, Husband D, Deshpande V et al (2020) LINE-1 ORF2p expression is nearly imperceptible in human cancers. Mob DNA 11:1

    Article  CAS  PubMed  Google Scholar 

  27. Briggs EM, Spadafora C, Logan SK (2019) A re-evaluation of LINE-1 ORF2 expression in LNCaP prostate cancer cells. Mob DNA 10:51

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Dai L, LaCava J, Taylor MS, Boeke JD (2014) Expression and detection of LINE-1 ORF-encoded proteins. Mob Genet Elements 4:e29319

    Article  PubMed  PubMed Central  Google Scholar 

  29. Kulpa DA, Moran JV (2005) Ribonucleoprotein particle formation is necessary but not sufficient for LINE-1 retrotransposition. Hum Mol Genet 14(21):3237–3248

    Article  CAS  PubMed  Google Scholar 

  30. Kulpa DA, Moran JV (2006) Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol 13(7):655–660

    Article  CAS  PubMed  Google Scholar 

  31. Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, Kazazian HH et al (2001) Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol 21(4):1429–1439

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Taylor MS, LaCava J, Mita P, Molloy KR, Huang CRL, Li D et al (2013) Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell 155(5):1034–1048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Arjan-Odedra S, Swanson CM, Sherer NM, Wolinsky SM, Malim MH (2012) Endogenous MOV10 inhibits the retrotransposition of endogenous retroelements but not the replication of exogenous retroviruses. Retrovirology 9:53

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Dai L, Taylor MS, O’Donnell KA, Boeke JD (2012) Poly(A) binding protein C1 is essential for efficient L1 retrotransposition and affects L1 RNP formation. Mol Cell Biol 32(21):4323–4336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Goodier JL, Cheung LE, Kazazian HH (2012) MOV10 RNA helicase is a potent inhibitor of retrotransposition in cells. PLoS Genet 8(10):e1002941

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Goodier JL, Cheung LE, Kazazian HH (2013) Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition. Nucleic Acids Res 41(15):7401–7419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Niewiadomska AM, Tian C, Tan L, Wang T, Sarkis PTN, Yu X-F (2007) Differential inhibition of long interspersed element 1 by APOBEC3 does not correlate with high-molecular-mass-complex formation or P-body association. J Virol 81(17):9577–9583

    Article  CAS  PubMed  Google Scholar 

  38. Suzuki J, Yamaguchi K, Kajikawa M, Ichiyanagi K, Adachi N, Koyama H et al (2009) Genetic evidence that the non-homologous end-joining repair pathway is involved in LINE retrotransposition. PLoS Genet 5(4):e1000461

    Article  PubMed  PubMed Central  Google Scholar 

  39. Peddigari S, Li PW-L, Rabe JL, Martin SL (2013) hnRNPL and nucleolin bind LINE-1 RNA and function as host factors to modulate retrotransposition. Nucleic Acids Res 41(1):575–585

    Article  CAS  PubMed  Google Scholar 

  40. Hata K, Sakaki Y (1997) Identification of critical CpG sites for repression of L1 transcription by DNA methylation. Gene 189(2):227–234

    Article  CAS  PubMed  Google Scholar 

  41. Soifer HS, Zaragoza A, Peyvan M, Behlke MA, Rossi JJ (2005) A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon. Nucleic Acids Res 33(3):846–856

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Yang N, Kazazian HH (2006) L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nat Struct Mol Biol 13(9):763–771

    Article  CAS  PubMed  Google Scholar 

  43. Mandal PK, Ewing AD, Hancks DC, Kazazian HH (2013) Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles. Hum Mol Genet 22(18):3730–3748

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Belancio VP, Whelton M, Deininger P (2007) Requirements for polyadenylation at the 3′ end of LINE-1 elements. Gene 390(1–2):98–107

    Article  CAS  PubMed  Google Scholar 

  45. Šulc P, Solovyov A, Marhon SA, Sun S, LaCava J, Abdel-Wahab O, et al. Repeats mimic immunostimulatory viral features across a vast evolutionary landscape. BioRxiv. 4 Nov 2021

    Google Scholar 

  46. De Cecco M, Ito T, Petrashen AP, Elias AE, Skvir NJ, Criscione SW et al (2019) L1 drives IFN in senescent cells and promotes age-associated inflammation. Nature 566(7742):73–78

    Article  PubMed  PubMed Central  Google Scholar 

  47. Malik HS, Burke WD, Eickbush TH (1999) The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol 16(6):793–805

    Article  CAS  PubMed  Google Scholar 

  48. 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(1):78–87

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Muotri AR, Chu VT, Marchetto MCN, Deng W, Moran JV, Gage FH (2005) Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435(7044):903–910

    Article  CAS  PubMed  Google Scholar 

  50. Taylor MS, Altukhov I, Molloy KR, Mita P, Jiang H, Adney EM et al (2018) Dissection of affinity captured LINE-1 macromolecular complexes. eLife 7:e30094

    Google Scholar 

  51. Wylie A, Jones AE, Abrams JM (2016) p53 in the game of transposons. BioEssays 38(11):1111–1116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Ardeljan D, Steranka JP, Liu C, Li Z, Taylor MS, Payer LM et al (2020) Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication. Nat Struct Mol Biol 27(2):168–178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Moldovan JB, Moran JV (2015) The zinc-finger antiviral protein ZAP inhibits LINE and Alu retrotransposition. PLoS Genet 11(5):e1005121

    Google Scholar 

  54. Pizarro JG, Cristofari G (2016) Post-transcriptional control of LINE-1 retrotransposition by cellular host factors in somatic cells. Front Cell Dev Biol 4:14

    Article  PubMed  PubMed Central  Google Scholar 

  55. Mita P, Wudzinska A, Sun X, Andrade J, Nayak S, Kahler DJ et al (2018) LINE-1 protein localization and functional dynamics during the cell cycle. eLife 7:e30058

    Google Scholar 

  56. Liu N, Lee CH, Swigut T, Grow E, Gu B, Bassik MC et al (2018) Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. Nature 553(7687):228–232

    Article  CAS  PubMed  Google Scholar 

  57. Vuong LM, Pan S, Donovan PJ (2019) Proteome profile of endogenous retrotransposon-associated complexes in human embryonic stem cells. Proteomics 19(15):e1900169

    Article  PubMed  PubMed Central  Google Scholar 

  58. Briggs EM, McKerrow W, Mita P, Boeke JD, Logan SK, Fenyö D (2021) RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs. Mob DNA 12(1):5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Garland W, Müller I, Wu M, Schmid M, Imamura K, Rib L et al (2022) Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression. Mol Cell 82(9):1691–1707.e8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. LaCava J, Jiang H, Rout MP (2016) Protein complex affinity capture from cryomilled mammalian cells. J Vis Exp 118:54518

    Google Scholar 

  61. Taylor MS, LaCava J, Dai L, Mita P, Burns KH, Rout MP et al (2016) Characterization of L1-ribonucleoprotein particles. Methods Mol Biol 1400:311–338

    Article  PubMed  PubMed Central  Google Scholar 

  62. Jiang H, Taylor MS, Molloy KR, Altukhov I, LaCava J (2019) Identification of RNase-sensitive LINE-1 ribonucleoprotein interactions by differential affinity immobilization. Bio Protoc 9(7):e3200

    Article  PubMed  PubMed Central  Google Scholar 

  63. Zougman A, Selby PJ, Banks RE (2014) Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis. Proteomics 14(9):1006–1000

    Article  CAS  PubMed  Google Scholar 

  64. Gagliardi M, Matarazzo MR (2016) RIP: RNA immunoprecipitation. Methods Mol Biol 1480:73–86

    Article  CAS  PubMed  Google Scholar 

  65. Maximum read length for illumina sequencing platforms [Internet]. [cited 2022 Apr 8]. Available from: https://support.illumina.com/bulletins/2020/04/maximum-read-length-for-illumina-sequencing-platforms.html

  66. McKerrow W, Fenyö D (2020) L1EM: a tool for accurate locus specific LINE-1 RNA quantification. Bioinformatics 36(4):1167–1173

    Article  CAS  PubMed  Google Scholar 

  67. Deininger P, Morales ME, White TB, Baddoo M, Hedges DJ, Servant G et al (2017) A comprehensive approach to expression of L1 loci. Nucleic Acids Res 45(5):e31

    Article  PubMed  Google Scholar 

  68. http://www.rstudio.com/ [Internet]. [cited 2022 Apr 8]. Available from: http://www.rstudio.com/

  69. Neuhauser N, Nagaraj N, McHardy P, Zanivan S, Scheltema R, Cox J et al (2013) High performance computational analysis of large-scale proteome data sets to assess incremental contribution to coverage of the human genome. J Proteome Res 12(6):2858–2868

    Article  CAS  PubMed  Google Scholar 

  70. Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 11(12):2301–2319

    Article  CAS  PubMed  Google Scholar 

  71. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367–1372

    Article  CAS  PubMed  Google Scholar 

  72. Bielow C, Mastrobuoni G, Kempa S (2016) Proteomics quality control: quality control software for maxquant results. J Proteome Res 15(3):777–787

    Article  CAS  PubMed  Google Scholar 

  73. Willforss J, Chawade A, Levander F (2019) NormalyzerDE: online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis. J Proteome Res 18(2):732–740

    Article  CAS  PubMed  Google Scholar 

  74. Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z et al (2021) clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (N Y) 2(3):100141

    CAS  Google Scholar 

  75. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15–21

    Article  CAS  PubMed  Google Scholar 

  76. Liao Y, Smyth GK, Shi W (2019) The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res 47(8):e47

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139–140

    Article  CAS  PubMed  Google Scholar 

  78. McCarthy DJ, Chen Y, Smyth GK (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res 40(10):4288–4297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Chen Y, Lun ATL, Smyth GK (2016) From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. [version 2; peer review: 5 approved]. F1000Res 5:1438

    PubMed  PubMed Central  Google Scholar 

  80. Leibold DM, Swergold GD, Singer MF, Thayer RE, Dombroski BA, Fanning TG (1990) Translation of LINE-1 DNA elements in vitro and in human cells. Proc Natl Acad Sci U S A 87(18):6990–6994

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Goodier JL, Zhang L, Vetter MR, Kazazian HH (2007) LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNA interference RNA-induced silencing complex. Mol Cell Biol 27(18):6469–6483

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Garcia-Perez JL, Morell M, Scheys JO, Kulpa DA, Morell S, Carter CC et al (2010) Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells. Nature 466(7307):769–773

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Philippe C, Vargas-Landin DB, Doucet AJ, van Essen D, Vera-Otarola J, Kuciak M et al (2016) Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci. eLife 5:e13926

    Google Scholar 

  84. Andrews PW, Goodfellow PN, Shevinsky LH, Bronson DL, Knowles BB (1982) Cell-surface antigens of a clonal human embryonal carcinoma cell line: morphological and antigenic differentiation in culture. Int J Cancer 29(5):523–531

    Article  CAS  PubMed  Google Scholar 

  85. Domanski M, Molloy K, Jiang H, Chait BT, Rout MP, Jensen TH et al (2012) Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels. BioTechniques 0(0):1–6

    PubMed  PubMed Central  Google Scholar 

  86. Obado SO, Field MC, Chait BT, Rout MP (2016) High-efficiency isolation of nuclear envelope protein complexes from trypanosomes. Methods Mol Biol 1411:67–80

    Article  CAS  PubMed  Google Scholar 

  87. Cristea IM, Chait BT (2011) Conjugation of magnetic beads for immunopurification of protein complexes. Cold Spring Harb Protoc 2011(5):pdb.prot5610

    Article  PubMed  PubMed Central  Google Scholar 

  88. Cristea IM, Williams R, Chait BT, Rout MP (2005) Fluorescent proteins as proteomic probes. Mol Cell Proteomics 4(12):1933–1941

    Article  CAS  PubMed  Google Scholar 

  89. LaCava J, Molloy KR, Taylor MS, Domanski M, Chait BT, Rout MP (2015) Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives. BioTechniques 58(3):103–119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Candiano G, Bruschi M, Musante L, Santucci L, Ghiggeri GM, Carnemolla B et al (2004) Blue silver: a very sensitive colloidal Coomassie G-250 staining for proteome analysis. Electrophoresis 25(9):1327–1333

    Article  CAS  PubMed  Google Scholar 

  91. Rosenberg IM (1996) Protein analysis and purification. Birkhäuser Boston, Boston

    Book  Google Scholar 

  92. Miller I, Crawford J, Gianazza E (2006) Protein stains for proteomic applications: which, when, why? Proteomics 6(20):5385–5408

    Article  CAS  PubMed  Google Scholar 

  93. Gauci VJ, Wright EP, Coorssen JR (2011) Quantitative proteomics: assessing the spectrum of in-gel protein detection methods. J Chem Biol 4(1):3–29

    Article  PubMed  Google Scholar 

  94. Piersma SR, Warmoes MO, de Wit M, de Reus I, Knol JC, Jiménez CR (2013) Whole gel processing procedure for GeLC-MS/MS based proteomics. Proteome Sci 11(1):17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1(6):2856–2860

    Article  CAS  PubMed  Google Scholar 

  96. Dunham WH, Mullin M, Gingras A-C (2012) Affinity-purification coupled to mass spectrometry: basic principles and strategies. Proteomics 12(10):1576–1590

    Article  CAS  PubMed  Google Scholar 

  97. Oeffinger M (2012) Two steps forward--one step back: advances in affinity purification mass spectrometry of macromolecular complexes. Proteomics 12(10):1591–1608

    Article  CAS  PubMed  Google Scholar 

  98. Dou Y, Kalmykova S, Pashkova M, Oghbaie M, Jiang H, Molloy KR et al (2020) Affinity proteomic dissection of the human nuclear cap-binding complex interactome. Nucleic Acids Res 48(18):10456–10469

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Wang X, Chambers MC, Vega-Montoto LJ, Bunk DM, Stein SE, Tabb DL (2014) QC metrics from CPTAC raw LC-MS/MS data interpreted through multivariate statistics. Anal Chem 86(5):2497–2509

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Bittremieux W, Tabb DL, Impens F, Staes A, Timmerman E, Martens L et al (2018) Quality control in mass spectrometry-based proteomics. Mass Spectrom Rev 37(5):697–711

    Article  CAS  PubMed  Google Scholar 

  101. Schurch NJ, Schofield P, Gierliński M, Cole C, Sherstnev A, Singh V et al (2016) How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA 22(6):839–851

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30(7):923–930

    Article  CAS  PubMed  Google Scholar 

  103. Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH (2019) SQuIRE reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Res 47(5):e27

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Jin Y, Tam OH, Paniagua E, Hammell M (2015) TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics 31(22):3593–3599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Chen D, Yang Z, Shen X, Sun L (2021) Capillary zone electrophoresis-tandem mass spectrometry as an alternative to liquid chromatography-tandem mass spectrometry for top-down proteomics of histones. Anal Chem 93(10):4417–4424

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Lubeckyj RA, Sun L (2022) Laser capture microdissection-capillary zone electrophoresis-tandem mass spectrometry (LCM-CZE-MS/MS) for spatially resolved top-down proteomics: a pilot study of zebrafish brain. Mol Omics 18(2):112–122

    Article  CAS  PubMed  Google Scholar 

  107. Charkow J, Röst HL (2021) Trapped ion mobility spectrometry reduces spectral complexity in mass spectrometry-based proteomics. Anal Chem 93(50):16751–16758

    Article  CAS  PubMed  Google Scholar 

  108. Gerbasi VR, Melani RD, Abbatiello SE, Belford MW, Huguet R, McGee JP et al (2021) Deeper protein identification using field asymmetric ion mobility spectrometry in top-down proteomics. Anal Chem 93(16):6323–6328

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Ihling CH, Piersimoni L, Kipping M, Sinz A (2021) Cross-linking/mass spectrometry combined with ion mobility on a timsTOF Pro instrument for structural proteomics. Anal Chem 93(33):11442–11450

    Article  CAS  PubMed  Google Scholar 

  110. Retsch GmbH. Ball Mills – guidelines for sample amount and ball charge. 19 July 2021. https://www.retsch.com/dltmp/www/5aba547e-5c30-40f3-9813-350c8ac9dd60-c416d7e1c7dd/info_ball_mills_ball_charge_en.pdf

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Acknowledgments

This work was supported in-part by National Institutes of Health grants R01GM126170 and P41GM109824.

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Di Stefano, L.H. et al. (2023). Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules. In: Branco, M.R., de Mendoza Soler, A. (eds) Transposable Elements. Methods in Molecular Biology, vol 2607. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2883-6_12

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  • DOI: https://doi.org/10.1007/978-1-0716-2883-6_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2882-9

  • Online ISBN: 978-1-0716-2883-6

  • eBook Packages: Springer Protocols

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