RNA–Protein: Comparison
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Please note this is a comparison between Version 2 by Camila Xu and Version 1 by André Gerber.

RNA–protein interactions are the nodes in a complex regulatory network that controls the fate of each RNA expressed in a cell.

  • RNA–protein interaction
  • non-coding RNA
  • RNA aptamer
  • antisense oligonucleotides
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References

  1. Uszczynska-Ratajczak, B.; Lagarde, J.; Frankish, A.; Guigo, R.; Johnson, R. Towards a complete map of the human long non-coding RNA transcriptome. Nat. Rev. Genet. 2018, 19, 535–548.
  2. Statello, L.; Guo, C.J.; Chen, L.L.; Huarte, M. Gene regulation by long non-coding RNAs and its biological functions. Nat. Rev. Mol. Cell Biol. 2021, 22, 96–118.
  3. Anantharaman, V.; Koonin, E.V.; Aravind, L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res. 2002, 30, 1427–1464.
  4. Gerstberger, S.; Hafner, M.; Tuschl, T. A census of human RNA-binding proteins. Nat. Rev. Genet. 2014, 15, 829–845.
  5. Gebauer, F.; Schwarzl, T.; Valcarcel, J.; Hentze, M.W. RNA-binding proteins in human genetic disease. Nat. Rev. Genet. 2020, 416–425.
  6. Iadevaia, V.; Gerber, A.P. Combinatorial Control of mRNA Fates by RNA-Binding Proteins and Non-Coding RNAs. Biomolecules 2015, 5, 2207–2222.
  7. Glisovic, T.; Bachorik, J.L.; Yong, J.; Dreyfuss, G. RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett. 2008, 582, 1977–1986.
  8. Corley, M.; Burns, M.C.; Yeo, G.W. How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms. Mol. Cell 2020, 78, 9–29.
  9. Albihlal, W.S.; Gerber, A.P. Unconventional RNA-binding proteins: An uncharted zone in RNA biology. FEBS Lett. 2018, 592, 2917–2931.
  10. Hentze, M.W.; Castello, A.; Schwarzl, T.; Preiss, T. A brave new world of RNA-binding proteins. Nat. Rev. Mol. Cell Biol. 2018, 19, 327–341.
  11. Tenenbaum, S.A.; Carson, C.C.; Lager, P.J.; Keene, J.D. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc. Natl. Acad. Sci. USA 2000, 97, 14085–14090.
  12. Gerber, A.P.; Herschlag, D.; Brown, P.O. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol. 2004, 2, E79.
  13. Nicholson, C.O.; Friedersdorf, M.; Keene, J.D. Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq. RNA 2017, 23, 32–46.
  14. Ule, J.; Jensen, K.B.; Ruggiu, M.; Mele, A.; Ule, A.; Darnell, R.B. CLIP identifies Nova-regulated RNA networks in the brain. Science 2003, 302, 1212–1215.
  15. Hafner, M.; Landthaler, M.; Burger, L.; Khorshid, M.; Hausser, J.; Berninger, P.; Rothballer, A.; Ascano, M., Jr.; Jungkamp, A.C.; Munschauer, M.; et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141, 129–141.
  16. Lee, F.C.Y.; Ule, J. Advances in CLIP Technologies for Studies of Protein-RNA Interactions. Mol. Cell 2018, 69, 354–369.
  17. Hogan, D.J.; Riordan, D.P.; Gerber, A.P.; Herschlag, D.; Brown, P.O. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol. 2008, 6, e255.
  18. Van Nostrand, E.L.; Freese, P.; Pratt, G.A.; Wang, X.; Wei, X.; Xiao, R.; Blue, S.M.; Chen, J.Y.; Cody, N.A.L.; Dominguez, D.; et al. A large-scale binding and functional map of human RNA-binding proteins. Nature 2020, 583, 711–719.
  19. Keene, J.D. RNA regulons: Coordination of post-transcriptional events. Nat. Rev. Genet. 2007, 8, 533–543.
  20. Imig, J.; Kanitz, A.; Gerber, A.P. RNA regulons and the RNA-protein interaction network. Biomol. Concepts 2012, 3, 403–414.
  21. Scherrer, T.; Mittal, N.; Janga, S.C.; Gerber, A.P. A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes. PLoS ONE 2010, 5, e15499.
  22. Tsvetanova, N.G.; Klass, D.M.; Salzman, J.; Brown, P.O. Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PLoS ONE 2010, 5, e12671.
  23. Baltz, A.G.; Munschauer, M.; Schwanhausser, B.; Vasile, A.; Murakawa, Y.; Schueler, M.; Youngs, N.; Penfold-Brown, D.; Drew, K.; Milek, M.; et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell 2012, 46, 674–690.
  24. Castello, A.; Fischer, B.; Eichelbaum, K.; Horos, R.; Beckmann, B.M.; Strein, C.; Davey, N.E.; Humphreys, D.T.; Preiss, T.; Steinmetz, L.M.; et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 2012, 149, 1393–1406.
  25. Beckmann, B.M.; Horos, R.; Fischer, B.; Castello, A.; Eichelbaum, K.; Alleaume, A.M.; Schwarzl, T.; Curk, T.; Foehr, S.; Huber, W.; et al. The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs. Nat. Commun. 2015, 6, 10127.
  26. Matia-Gonzalez, A.M.; Laing, E.E.; Gerber, A.P. Conserved mRNA-binding proteomes in eukaryotic organisms. Nat. Struct. Mol. Biol. 2015, 22, 1027–1033.
  27. Perez-Perri, J.I.; Rogell, B.; Schwarzl, T.; Stein, F.; Zhou, Y.; Rettel, M.; Brosig, A.; Hentze, M.W. Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture. Nat. Commun. 2018, 9, 4408.
  28. Queiroz, R.M.L.; Smith, T.; Villanueva, E.; Marti-Solano, M.; Monti, M.; Pizzinga, M.; Mirea, D.M.; Ramakrishna, M.; Harvey, R.F.; Dezi, V.; et al. Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS). Nat. Biotechnol. 2019, 37, 169–178.
  29. Urdaneta, E.C.; Vieira-Vieira, C.H.; Hick, T.; Wessels, H.H.; Figini, D.; Moschall, R.; Medenbach, J.; Ohler, U.; Granneman, S.; Selbach, M.; et al. Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. Nat. Commun. 2019, 10, 990.
  30. Trendel, J.; Schwarzl, T.; Horos, R.; Prakash, A.; Bateman, A.; Hentze, M.W.; Krijgsveld, J. The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest. Cell 2019, 176, 391–403.e19.
  31. Bao, X.; Guo, X.; Yin, M.; Tariq, M.; Lai, Y.; Kanwal, S.; Zhou, J.; Li, N.; Lv, Y.; Pulido-Quetglas, C.; et al. Capturing the interactome of newly transcribed RNA. Nat. Methods 2018, 15, 213–220.
  32. Huang, R.; Han, M.; Meng, L.; Chen, X. Transcriptome-wide discovery of coding and noncoding RNA-binding proteins. Proc. Natl. Acad. Sci. USA 2018, 115, E3879–E3887.
  33. Castello, A.; Fischer, B.; Frese, C.K.; Horos, R.; Alleaume, A.M.; Foehr, S.; Curk, T.; Krijgsveld, J.; Hentze, M.W. Comprehensive Identification of RNA-Binding Domains in Human Cells. Mol. Cell 2016, 63, 696–710.
  34. Shchepachev, V.; Bresson, S.; Spanos, C.; Petfalski, E.; Fischer, L.; Rappsilber, J.; Tollervey, D. Defining the RNA interactome by total RNA-associated protein purification. Mol. Syst. Biol. 2019, 15, e8689.
  35. Bae, J.W.; Kwon, S.C.; Na, Y.; Kim, V.N.; Kim, J.S. Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid resolution. Nat. Struct. Mol. Biol. 2020, 27, 678–682.
  36. Ramanathan, M.; Porter, D.F.; Khavari, P.A. Methods to study RNA-protein interactions. Nat. Methods 2019, 16, 225–234.
  37. Van Ende, R.; Balzarini, S.; Geuten, K. Single and Combined Methods to Specifically or Bulk-Purify RNA-Protein Complexes. Biomolecules 2020, 10, 1160.
  38. Dasti, A.; Cid-Samper, F.; Bechara, E.; Tartaglia, G.G. RNA-centric approaches to study RNA-protein interactions in vitro and in silico. Methods 2020, 178, 11–18.
  39. Strehle, M.; Guttman, M. Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation. Curr. Opin. Cell Biol. 2020, 64, 139–147.
  40. Schwartz, J.C.; Wang, X.; Podell, E.R.; Cech, T.R. RNA seeds higher-order assembly of FUS protein. Cell Rep. 2013, 5, 918–925.
  41. Zhang, L.; Zhang, K.; Prandl, R.; Schoffl, F. Detecting DNA-binding of proteins in vivo by UV-crosslinking and immunoprecipitation. Biochem. Biophys. Res. Commun. 2004, 322, 705–711.
  42. Gemmill, D.; D’Souza, S.; Meier-Stephenson, V.; Patel, T.R. Current approaches for RNA-labelling to identify RNA-binding proteins. Biochem. Cell Biol. 2020, 98, 31–41.
  43. Hamasaki, K.; Killian, J.; Cho, J.; Rando, R.R. Minimal RNA constructs that specifically bind aminoglycoside antibiotics with high affinities. Biochemistry 1998, 37, 656–663.
  44. Bachler, M.; Schroeder, R.; von Ahsen, U. StreptoTag: A novel method for the isolation of RNA-binding proteins. RNA 1999, 5, 1509–1516.
  45. Hartmuth, K.; Vornlocher, H.P.; Luhrmann, R. Tobramycin affinity tag purification of spliceosomes. Methods Mol. Biol. 2004, 257, 47–64.
  46. Vazquez-Pianzola, P.; Urlaub, H.; Rivera-Pomar, R. Proteomic analysis of reaper 5’ untranslated region-interacting factors isolated by tobramycin affinity-selection reveals a role for La antigen in reaper mRNA translation. Proteomics 2005, 5, 1645–1655.
  47. Windbichler, N.; Schroeder, R. Isolation of specific RNA-binding proteins using the streptomycin-binding RNA aptamer. Nat. Protoc. 2006, 1, 637–640.
  48. Iadevaia, V.; Wouters, M.D.; Kanitz, A.; Matia-Gonzalez, A.M.; Laing, E.E.; Gerber, A.P. Tandem RNA isolation reveals functional rearrangement of RNA-binding proteins on CDKN1B/p27(Kip1) 3’UTRs in cisplatin treated cells. RNA Biol. 2020, 17, 33–46.
  49. Slobodin, B.; Gerst, J.E. A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes. RNA 2010, 16, 2277–2290.
  50. Leppek, K.; Stoecklin, G. An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins. Nucleic Acids Res. 2014, 42, e13.
  51. Hogg, J.R.; Collins, K. RNA-based affinity purification reveals 7SK RNPs with distinct composition and regulation. RNA 2007, 13, 868–880.
  52. Di Tomasso, G.; Jenkins, L.M.M.; Legault, P. ARiBo pull-down for riboproteomic studies based on label-free quantitative mass spectrometry. RNA 2016, 22, 1760–1770.
  53. Lee, H.Y.; Haurwitz, R.E.; Apffel, A.; Zhou, K.; Smart, B.; Wenger, C.D.; Laderman, S.; Bruhn, L.; Doudna, J.A. RNA-protein analysis using a conditional CRISPR nuclease. Proc. Natl. Acad. Sci. USA 2013, 110, 5416–5421.
  54. McDermott, J.J.; Watkins, K.P.; Williams-Carrier, R.; Barkan, A. Ribonucleoprotein Capture by in Vivo Expression of a Designer Pentatricopeptide Repeat Protein in Arabidopsis. Plant Cell 2019, 31, 1723–1733.
  55. Scherer, M.; Levin, M.; Butter, F.; Scheibe, M. Quantitative Proteomics to Identify Nuclear RNA-Binding Proteins of Malat1. Int. J. Mol. Sci. 2020, 21, 1166.
  56. Faoro, C.; Ataide, S.F. Ribonomic approaches to study the RNA-binding proteome. FEBS Lett. 2014, 588, 3649–3664.
  57. Hogg, J.R.; Goff, S.P. Upf1 senses 3’UTR length to potentiate mRNA decay. Cell 2010, 143, 379–389.
  58. Tsai, B.P.; Wang, X.; Huang, L.; Waterman, M.L. Quantitative profiling of in vivo-assembled RNA-protein complexes using a novel integrated proteomic approach. Mol. Cell. Proteom. 2011, 10, M110.007385.
  59. Yoon, J.H.; Gorospe, M. Identification of mRNA-Interacting Factors by MS2-TRAP (MS2-Tagged RNA Affinity Purification). Methods Mol. Biol. 2016, 1421, 15–22.
  60. Ramanathan, M.; Majzoub, K.; Rao, D.S.; Neela, P.H.; Zarnegar, B.J.; Mondal, S.; Roth, J.G.; Gai, H.; Kovalski, J.R.; Siprashvili, Z.; et al. RNA-protein interaction detection in living cells. Nat. Methods 2018, 15, 207–212.
  61. Blencowe, B.J.; Sproat, B.S.; Ryder, U.; Barabino, S.; Lamond, A.I. Antisense probing of the human U4/U6 snRNP with biotinylated 2’-OMe RNA oligonucleotides. Cell 1989, 59, 531–539.
  62. Lingner, J.; Cech, T.R. Purification of telomerase from Euplotes aediculatus: Requirement of a primer 3’ overhang. Proc. Natl. Acad. Sci. USA 1996, 93, 10712–10717.
  63. Schnapp, G.; Rodi, H.P.; Rettig, W.J.; Schnapp, A.; Damm, K. One-step affinity purification protocol for human telomerase. Nucleic Acids Res. 1998, 26, 3311–3313.
  64. West, J.A.; Davis, C.P.; Sunwoo, H.; Simon, M.D.; Sadreyev, R.I.; Wang, P.I.; Tolstorukov, M.Y.; Kingston, R.E. The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Mol. Cell 2014, 55, 791–802.
  65. Chu, C.; Zhang, Q.C.; da Rocha, S.T.; Flynn, R.A.; Bharadwaj, M.; Calabrese, J.M.; Magnuson, T.; Heard, E.; Chang, H.Y. Systematic discovery of Xist RNA binding proteins. Cell 2015, 161, 404–416.
  66. Kim, J.; Piao, H.L.; Kim, B.J.; Yao, F.; Han, Z.; Wang, Y.; Xiao, Z.; Siverly, A.N.; Lawhon, S.E.; Ton, B.N.; et al. Long noncoding RNA MALAT1 suppresses breast cancer metastasis. Nat. Genet. 2018, 50, 1705–1715.
  67. McHugh, C.A.; Chen, C.K.; Chow, A.; Surka, C.F.; Tran, C.; McDonel, P.; Pandya-Jones, A.; Blanco, M.; Burghard, C.; Moradian, A.; et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 2015, 521, 232–236.
  68. Minajigi, A.; Froberg, J.; Wei, C.; Sunwoo, H.; Kesner, B.; Colognori, D.; Lessing, D.; Payer, B.; Boukhali, M.; Haas, W.; et al. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science 2015, 349.
  69. Spiniello, M.; Knoener, R.A.; Steinbrink, M.I.; Yang, B.; Cesnik, A.J.; Buxton, K.E.; Scalf, M.; Jarrard, D.F.; Smith, L.M. HyPR-MS for Multiplexed Discovery of MALAT1, NEAT1, and NORAD lncRNA Protein Interactomes. J. Proteome Res. 2018, 17, 3022–3038.
  70. Knoener, R.A.; Becker, J.T.; Scalf, M.; Sherer, N.M.; Smith, L.M. Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry. Sci. Rep. 2017, 7, 16965.
  71. Spiniello, M.; Steinbrink, M.I.; Cesnik, A.J.; Miller, R.M.; Scalf, M.; Shortreed, M.R.; Smith, L.M. Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. RNA 2019, 25, 1337–1352.
  72. Upadhyay, A.; Dixit, U.; Manvar, D.; Chaturvedi, N.; Pandey, V.N. Affinity capture and identification of host cell factors associated with hepatitis C virus (+) strand subgenomic RNA. Mol. Cell. Proteom. 2013, 12, 1539–1552.
  73. Lenarcic, E.M.; Landry, D.M.; Greco, T.M.; Cristea, I.M.; Thompson, S.R. Thiouracil cross-linking mass spectrometry: A cell-based method to identify host factors involved in viral amplification. J. Virol. 2013, 87, 8697–8712.
  74. Phillips, S.L.; Soderblom, E.J.; Bradrick, S.S.; Garcia-Blanco, M.A. Identification of Proteins Bound to Dengue Viral RNA In Vivo Reveals New Host Proteins Important for Virus Replication. MBio 2016, 7, e01865-15.
  75. Matia-Gonzalez, A.M.; Iadevaia, V.; Gerber, A.P. A versatile tandem RNA isolation procedure to capture in vivo formed mRNA-protein complexes. Methods 2017, 118, 93–100.
  76. Rogell, B.; Fischer, B.; Rettel, M.; Krijgsveld, J.; Castello, A.; Hentze, M.W. Specific RNP capture with antisense LNA/DNA mixmers. RNA 2017, 23, 1290–1302.
  77. Theil, K.; Imami, K.; Rajewsky, N. Identification of proteins and miRNAs that specifically bind an mRNA in vivo. Nat. Commun. 2019, 10, 4205.
  78. Chu, C.; Spitale, R.C.; Chang, H.Y. Technologies to probe functions and mechanisms of long noncoding RNAs. Nat. Struct. Mol. Biol. 2015, 22, 29–35.
  79. Simon, M.D.; Wang, C.I.; Kharchenko, P.V.; West, J.A.; Chapman, B.A.; Alekseyenko, A.A.; Borowsky, M.L.; Kuroda, M.I.; Kingston, R.E. The genomic binding sites of a noncoding RNA. Proc. Natl. Acad. Sci. USA 2011, 108, 20497–20502.
  80. Chu, C.; Qu, K.; Zhong, F.L.; Artandi, S.E.; Chang, H.Y. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 2011, 44, 667–678.
  81. Engreitz, J.M.; Pandya-Jones, A.; McDonel, P.; Shishkin, A.; Sirokman, K.; Surka, C.; Kadri, S.; Xing, J.; Goren, A.; Lander, E.S.; et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 2013, 341, 1237973.
  82. Kazimierczyk, M.; Kasprowicz, M.K.; Kasprzyk, M.E.; Wrzesinski, J. Human Long Noncoding RNA Interactome: Detection, Characterization and Function. Int. J. Mol. Sci. 2020, 21, 1027.
  83. Harris, D.; Zhang, Z.; Chaubey, B.; Pandey, V.N. Identification of cellular factors associated with the 3’-nontranslated region of the hepatitis C virus genome. Mol. Cell. Proteom. 2006, 5, 1006–1018.
  84. Zeng, F.; Peritz, T.; Kannanayakal, T.J.; Kilk, K.; Eiriksdottir, E.; Langel, U.; Eberwine, J. A protocol for PAIR: PNA-assisted identification of RNA binding proteins in living cells. Nat. Protoc. 2006, 1, 920–927.
  85. Phillips, S.L.; Garcia-Blanco, M.A.; Bradrick, S.S. Antisense-mediated affinity purification of dengue virus ribonucleoprotein complexes from infected cells. Methods 2015, 91, 13–19.
  86. Tan, C.C.S.; Maurer-Stroh, S.; Wan, Y.; Sessions, O.M.; de Sessions, P.F. A novel method for the capture-based purification of whole viral native RNA genomes. AMB Express 2019, 9, 45.
  87. Hassan, T.; Smith, S.G.; Gaughan, K.; Oglesby, I.K.; O’Neill, S.; McElvaney, N.G.; Greene, C.M. Isolation and identification of cell-specific microRNAs targeting a messenger RNA using a biotinylated anti-sense oligonucleotide capture affinity technique. Nucleic Acids Res. 2013, 41, e71.
  88. Iadevaia, V.; Matia-Gonzalez, A.M.; Gerber, A.P. An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes. J. Vis. Exp. 2018, 58223.
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