Journal of Applied Biological Chemistry

  • 제58권3호
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  • Pages.201-208
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  • 2015
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  • 1976-0442(pISSN)
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  • 2234-7941(eISSN)
한국응용생명화학회 (The Korean Society for Applied Biological Chemistry)
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RNA 결합 단백질과 유전자 발현조절

RNA Binding Proteins and its Regulation of Gene Expression

  • Roh, Kyung Hee (Department of metabolic engineering, National Academy of Agricultural Science, Rural Development Administration) ;
  • Kang, Han-Chul (Department of metabolic engineering, National Academy of Agricultural Science, Rural Development Administration) ;
  • Kim, Jong-Bum (Department of metabolic engineering, National Academy of Agricultural Science, Rural Development Administration) ;
  • Kim, Hyun-UK (Department of metabolic engineering, National Academy of Agricultural Science, Rural Development Administration) ;
  • Lee, Kyung-Ryeol (Department of metabolic engineering, National Academy of Agricultural Science, Rural Development Administration) ;
  • Kim, Sun Hee (Department of metabolic engineering, National Academy of Agricultural Science, Rural Development Administration)
  • 투고 : 2015.01.29
  • 심사 : 2015.03.19
  • 발행 : 2015.09.30
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⟨ 이전 논문 다음 논문 ⟩

초록

RNA 결합 단백질들이 유전자 조절의 다양한 범위에 작용한다는 사실이 아주 중요하다. 유전자의 전사에 관련된 유전자 조절이 많이 연구가 되었어도 RNA의 조절에 관한 연구는 상대적으로 부진한 편이다. RNA 결합 단백질들은 RNA와 관련되는 각종 과정, 예를 들면 전사, pre-mRNA splicing, polyadenylation, 수송, 위치화, 번역, 분해 및 구조의 유지 등 다양한 범위에서 작용을 하고 있다. RNA 결합 단백질들의 많은 부분들이 아직 잘 알려지지 않고 있으며 유전자 발현에 대해 더 잘 이해하기 위해 이러한 부분의 연구가 더 수행되어야 한다. 최근에 유전학, 생화 학, 및 유전자들의 생물정보학의 발달 등으로 인하여. RNA 결합 단백질들의 다양한 분야들이 알려지고 있으며 이러한 부분들이 많은 관심을 받고 있다.

The role of RNA-binding proteins (RBPs) to regulate expression of genes seems to be very important. RBPs play important roles in RNA related bioprocess such as transcription, pre-mRNA splicing, polyadenylation, transport, localization, translation, turn over and maintenance of structure. Despite of many researches on RNA binding proteins, detailed mechanisms of these proteins have not been fully understood. It seems that many parts of RBPs remains unknown and should be characterized for the better understanding of gene expression. Recently, genetic, biochemical, and bioinformatic analysis of genomes revealed a vast array of RBPs and many parts are interesting to understand bioprocessing including gene expression.

키워드

참고문헌

  1. Auweter S, Oberstrass FC, and Allain FH (2006) Sequence-specific binding of single-stranded RNA: is there a code for recognition? Nucleic Acids Res 34, 4943-59. https://doi.org/10.1093/nar/gkl620
  2. Bandziulis RJ, Swanson MS, and Dreyfuss G (1989) RNA-binding proteins as developmental regulators. Genes Dev 3, 431-7. https://doi.org/10.1101/gad.3.4.431
  3. Bienroth S, Wahle E, Suter-Crazzolara C, and Keller W (1991) Purification of the cleavage and poly-adenylation factor involved in the 3'-processing of messenger RNA precursors. J Biol Chem 266, 19768-76.
  4. Blaszczyk J, Gan J, Tropea JE, Court DL, Waugh DS, and Ji X (2004) Noncatalytic assembly of ribonuclease III with doublestranded RNA. Structure 12, 457-66. https://doi.org/10.1016/j.str.2004.02.004
  5. Blencowe BJ (2006) Alternative splicing: new insights from global analyses. Cell 126, 37-47. https://doi.org/10.1016/j.cell.2006.06.023
  6. Bomsztyk K, Denisenko O, and Ostrowski J (2004) One protein multiple process. Bioessays 26, 629-38. https://doi.org/10.1002/bies.20048
  7. Brown EC and Jackson RJ (2004) All five cold-shock domains of unr (upstream of N-ras) are required for stimulation of human rhinovirus RNA translation. J Gen Virol 85, 2279-87. https://doi.org/10.1099/vir.0.80045-0
  8. Carroll D (2011) Genome engineering with zinc-finger nucleases. Genetics 188, 773-82. https://doi.org/10.1534/genetics.111.131433
  9. Chaudhury A, Chander P, and Howe P (2010) Heterogeneous nuclear ribonucleoproteins in cellular processes. RNA 16, 1449-62. https://doi.org/10.1261/rna.2254110
  10. Chen Y and Varani G (2005) Protein families and RNA recognition. FEBS J 272, 2088-97. https://doi.org/10.1111/j.1742-4658.2005.04650.x
  11. Cheong CG and Hall TM (2006) Engineering RNA sequence specificity of Pumilio repeats. Proc Natl Acad Sci USA 103, 13635-9. https://doi.org/10.1073/pnas.0606294103
  12. Cruz-herrera C, Campagna M, Garcia M, and Villar L (2014) Activation of the double stranded RNA-dependent protein kinase PKR by sumo. J Biol Chem 29, 1-19.
  13. Daubner G, Clery A, and Allan F (2013) RRM-RNA recognition; NMR or crystallography. Curr Opi Struc Biol 23, 100-8. https://doi.org/10.1016/j.sbi.2012.11.006
  14. Dictenberg, Jason B, Swanger SA, Antar LN, Singer RH, and Bassel GJ (2008) A direct role for FMRP in activity-dependent dendritic mRNA transport links filopodial-spine morphogenesis to fragile X syndrome. Dev Cell 14, 926-39. https://doi.org/10.1016/j.devcel.2008.04.003
  15. Dreyfuss G, Kim VN, and Kataoka N (2002) Messenger-RNA-binding proteins and the messages they carry. Nature Reviews Mol Cell Biol 3, 195-205. https://doi.org/10.1038/nrm760
  16. Edwards TA, Pyle SE, Wharton RP, and Aggarwal AK (2001) Structure of Pumilio reveals similarity between RNA and peptide binding motifs. Cell 105, 281-9. https://doi.org/10.1016/S0092-8674(01)00318-X
  17. Ernst RK, Bray M, Rekosh D, and Hammarskjold ML (1997) A structured retroviral RNA element that mediates nucleocytoplasmic export of intron-containing RNA. Mol Cell Biol 17, 135-44. https://doi.org/10.1128/MCB.17.1.135
  18. Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, and Ji X (2006) Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell 124, 355-66. https://doi.org/10.1016/j.cell.2005.11.034
  19. Glisovic T, Bachorik JL, Yong J, and Dreyfuss G (2008) RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett 582, 1977-86. https://doi.org/10.1016/j.febslet.2008.03.004
  20. Gruter P, Carlos T, and Cayetato K (1998) TAP, the human homolog of Mex67p, mediates CTE-dependent RNA export from the nucleus. Mol Cell 1, 649-59. https://doi.org/10.1016/S1097-2765(00)80065-9
  21. Guil S and Caceres JF (2007) The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat Struct Mol Biol 14, 591-6. https://doi.org/10.1038/nsmb1250
  22. Halbeisen RE, Galgano A, Scherrer T, and Gerber AP (2008) Posttranscriptional gene regulation: from genome-wide studies to principles. Cell Mol Life Sci 65, 798-813. https://doi.org/10.1007/s00018-007-7447-6
  23. Hieronymus H and Silver PA (2004) A systematic view of mRNP biology. Genes Dev 18, 2845-60. https://doi.org/10.1101/gad.1256904
  24. Higuchi M, Single FN, Kohler M, Sommer B, Sprengel R, and Seeburg PH (1993) RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency. Cell 75, 1361-70. https://doi.org/10.1016/0092-8674(93)90622-W
  25. Hoopengardner B, Bhalla T, Staber C, and Reenan R (2003) Nervous system targets of RNA editing identified by comparative genomics. Science 301, 832-6. https://doi.org/10.1126/science.1086763
  26. Hou VC, Komili S, and Casolari JM (2002) Decrease in hnRNP A/B expression during erythropoiesis mediates a pre-mRNA splicing switch. EMBO J 21, 6195-204. https://doi.org/10.1093/emboj/cdf625
  27. Huang Y, Ji L, Huang Q, Vassylyev DG, Chen X, and Ma J-B (2009) Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 461, 823-7. https://doi.org/10.1038/nature08433
  28. Inbal P, Idit K, Manuel A, and Melissa C (2014) RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res 14, 1-7.
  29. Katahira J, Strasser K, Podtelejnikov A, Mann M, and Jung JU (1999) The Mex67p-mediated nuclear mRNA export pathway is conserved from yeast to human. EMBO J 18, 2593-609. https://doi.org/10.1093/emboj/18.9.2593
  30. Keene JD (2001) Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc Natl Acad Sci USA 98, 7018-24. https://doi.org/10.1073/pnas.111145598
  31. Keene JD (2007) RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 8, 533-43. https://doi.org/10.1038/nrg2111
  32. Keene JD and Tenenbaum SA (2002) Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell 9, 1161-7. https://doi.org/10.1016/S1097-2765(02)00559-2
  33. Kharrat A, Macias MJ, and Gibson TJ (1995) Structure of the dsRNA binding domain of E. coli RNase III. EMBO J 14, 3572-84.
  34. Lasko P (2000) The drosophila melanogaster genome: translation factors and RNA binding proteins. J Cell Biol 150, 51-6. https://doi.org/10.1083/jcb.150.2.F51
  35. Lecuyer E, Yoshida H, Parthasarathy N, Alm C, and Babak T (2007) Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 131, 174-87. https://doi.org/10.1016/j.cell.2007.08.003
  36. Leffers H, Dejgaard K, and Celis JE (1995) Characterisation of two major cellular poly(rC)-binding human proteins, each containing three Khomologous (KH) domains. Eur J Biochem 230, 447-53. https://doi.org/10.1111/j.1432-1033.1995.tb20581.x
  37. Legendre JB, Campbell ZT, and Conner P (2013) RNA targets and specificity of Staufen, a double-stranded RNA-binding protein in Caenorhabditis elegans. J Biol Chem 288, 2532-45. https://doi.org/10.1074/jbc.M112.397349
  38. Lunde BM, Moore C, and Varani G (2007) RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol 8, 479-90. https://doi.org/10.1038/nrm2178
  39. Maris C, Dominguez C, and Allain FH (2005) The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J 272, 2118-31. https://doi.org/10.1111/j.1742-4658.2005.04653.x
  40. Matera AG, Terns RM, and Terns MP (2007) Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol 8, 209-20. https://doi.org/10.1038/nrm2124
  41. Meister G (2013) Argonaute proteins ; functional insight and emerging roles. Nature Rev Gen 14, 447-59. https://doi.org/10.1038/nrg3462
  42. Mili S and Steitz JA (2004) Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA 10, 1692-4. https://doi.org/10.1261/rna.7151404
  43. Moore MJ (2005) From birth to death; the complex lives of eukaryotic mRNAs. Science 309, 1514-8. https://doi.org/10.1126/science.1111443
  44. Nanduri S, Carpick B, and Yang Y (1998) Structure of the doublestranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation. EMBO J 17, 5458-65. https://doi.org/10.1093/emboj/17.18.5458
  45. Narva E, Rankonen E, Emani MR, and Lund R (2012) RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem cell 30, 452-60. https://doi.org/10.1002/stem.1013
  46. Niranjanakumari S, Lasda E, and Brazas R (2002) Reversible cross-linking combined with immunoprecipitation to study RNA-protein interactions in vivo. Methods 26, 182-90. https://doi.org/10.1016/S1046-2023(02)00021-X
  47. Nishikura K (2006) Editor meets silencer: crosstalk between RNA editing and RNA interference. Nat Rev Mol Cell Biol 7, 919-31. https://doi.org/10.1038/nrm2061
  48. Opperman L, Hook B, DeFino M, Bernstein DS, and Wickens M (2005) A single spacer nucleotide determines the specificities of two mRNA regulatory proteins. Nat Struct Mol Biol 12, 945-51. https://doi.org/10.1038/nsmb1010
  49. Ostrowski J, Sims JE, Sibley CH, Valentine MA, and Dower SK (1991) A serine/threonine kinase activity is closely associated with a 65-kDa phosphoprotein specifically recognized by the kappa B enhancer element. J Biol Chem 266, 12722-33.
  50. Park JE, Heo I, Tian Y, and Simanshu D, and Kim VN (2011) Dicer recognizes the 5' end of RNA for efficient RNA processing. Nature 475, 201-5 https://doi.org/10.1038/nature10198
  51. Patino C, Haenni AL, and Urcucqui S (2014) NF90 isoforms, a new family of cellular proteins involved in viral replication? Biochimie 4, 20-4.
  52. Perreault A, Lemieux C, and Bachand F (2007) Regulation of the nuclear poly(A)-binding protein by arginine methylation in fission yeast. J Biol Chem 282, 7552-62. https://doi.org/10.1074/jbc.M610512200
  53. Pleiss JA, Whitworth GB, Bergkessel M, and Guthrie C (2007) Rapid, transcript specific changes in splicing in response to environmental stress. Mol Cell 2, 928-37.
  54. Ramos A, Grunert S, Adams J, Micklem DR, and Proctor MR (2000) RNA recognition by a Staufen double-stranded RNA-binding domain. EMBO J 19, 997-1009. https://doi.org/10.1093/emboj/19.5.997
  55. Redfern AD, Colley SM, and Beveridge DJ (2013) RNA-induced silencing complex (RISC) Proteins PACT, TRBP, and Dicer are SRA binding nuclear receptor coregulators. Proc Natl Acad Sci USA 16, 6536-41.
  56. Ryan K, Calvo O, and Manley JL (2004) Evidence that polyadenylation factor CPSF-73 is the mRNA 3' processing endonuclease. RNA 10, 565-73. https://doi.org/10.1261/rna.5214404
  57. Santos-Rosa H, Moreno H, Simos G, Segref A, Fahrenkrog B, and Pante N (1998) Nuclear mRNA export requires complex formation between Mex67p and Mtr2p at the nuclear pores. Mol Cell Biol 8, 6826-38.
  58. Schullery DS, Ostrowski J, Denisenko ON, Stempka L, Shnyreva M, and Suzuki H (1999) Regulated interaction of protein kinase Cdelta with the heterogeneous nuclear ribonucleoprotein K protein. J Biol Chem 274, 15101-9. https://doi.org/10.1074/jbc.274.21.15101
  59. Shen EC, Henry MF, Weiss VH, Valentini SR, and Silver PA (1998) Arginine methylation facilitates the nuclear export of hnRNP proteins. Genes Dev 12, 679-91. https://doi.org/10.1101/gad.12.5.679
  60. Shen R, Weng C, Yu J, and Xie T (2009) elF4a controls germline stem cell self-renewal by directly binding BAM function in the Drosophila ovary. Proc Natl Acad Sci USA 106, 11623-8. https://doi.org/10.1073/pnas.0903325106
  61. Stefl R, Oberstrass FC, Hood JL, Jourdan M, Zimmermann M, and Skrisovska L (2010) The solution structure of the ADAR2 dsRBM-RNA complex reveals a sequence-specific readout of the minor groove. Cell 143, 225-37. https://doi.org/10.1016/j.cell.2010.09.026
  62. Stefl R, Skrisovska L, and Allain F (2005) RNA sequence and shape dependent recognition by proteins in the ribonucleoprotein particle. EMBO Reports 6, 33-8. https://doi.org/10.1038/sj.embor.7400325
  63. Stutz F, Bachi A, Doerks T, Braun IC, Seraphin B, and Wilm M (2000) REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. RNA 6, 638-50. https://doi.org/10.1017/S1355838200000078
  64. Taniguchi I and Ohno M (2008) ATP-dependent recruitment of export factor Aly/REF onto intronless mRNAs by RNA helicase UAP56. Mol Cell Biol 28, 601-8. https://doi.org/10.1128/MCB.01341-07
  65. Thakur M, Seo EJ, and Dever TE (2013) Variola virus E3L Za domain but not its Z-DNA binding activity is required for PKR inhibition. RNA 23, 1-14.
  66. Valente L and Nishikura K (2005) ADAR gene family and A-to-I RNA editing: diverse roles in posttranscriptional gene regulation. Prog Nucleic Acid Res Mol Biol 79, 299-38. https://doi.org/10.1016/S0079-6603(04)79006-6
  67. Vassileva MT and Matunis MJ (2004) SUMO modification of heterogeneous nuclear ribonucleo-proteins. Mol Cell Biol 24, 3623-32. https://doi.org/10.1128/MCB.24.9.3623-3632.2004
  68. Wahle E and Ruegsegger U (1999) 3'-End processing of pre-mRNA in eukaryotes. FEMS Microbiol Rev 23, 277-95. https://doi.org/10.1111/j.1574-6976.1999.tb00400.x
  69. Wang X, McLachlan J, Zamore PD, and Hall TM (2002) Modular recognition of RNA by a human pum-iliohomology domain. Cell 110, 501-12. https://doi.org/10.1016/S0092-8674(02)00873-5
  70. Wang X, Zamore PD, and Hall TM (2001) Crystal structure of a Pumilio homology domain. Mol Cell 7, 855-65. https://doi.org/10.1016/S1097-2765(01)00229-5
  71. Yang SW, Chen H-Y, Yang J, Machida S, Chua N-H, and Yuan YA (2010) Structure of Arabidopsis HYPONASTICLEAVES1 and its molecular implications for miRNA processing. Structure 18, 594-605. https://doi.org/10.1016/j.str.2010.02.006
  72. Yu MC, Bachand F, McBride AE, Komili S, and Casolari JM (2004) Arginine methyltransferase affects interactions and recruitment of mRNA processing and export factors. Genes Dev 18, 2024-35. https://doi.org/10.1101/gad.1223204
  73. Zhang QS, Manche L, Xu RM, and Krainer AR (2006) hnRNP A1 associates with telomere ends and stimulates telomerase activity. RNA 12, 1116-28. https://doi.org/10.1261/rna.58806