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Nature communications
08 25, 2021;12 (1): 5120.

A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome.

Doyeon Kim, Sukjun Kim, Joori Park, Hee Ryung Chang, Jeeyoon Chang, Junhak Ahn, Heedo Park, Junehee Park, Narae Son, Gihyeon Kang, Jeonghun Kim, Kisoon Kim, Man-Seong Park, Yoon Ki Kim, Daehyun Baek
Author Information
  1. Doyeon Kim: School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
  2. Sukjun Kim: School of Biological Sciences, Seoul National University, Seoul, Republic of Korea. ORCID
  3. Joori Park: Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, Republic of Korea. ORCID
  4. Hee Ryung Chang: School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
  5. Jeeyoon Chang: Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, Republic of Korea. ORCID
  6. Junhak Ahn: School of Biological Sciences, Seoul National University, Seoul, Republic of Korea. ORCID
  7. Heedo Park: Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea. ORCID
  8. Junehee Park: School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
  9. Narae Son: School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
  10. Gihyeon Kang: School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
  11. Jeonghun Kim: Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea. ORCID
  12. Kisoon Kim: Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea.
  13. Man-Seong Park: Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea. manseong.park@gmail.com.
  14. Yoon Ki Kim: Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, Republic of Korea. yk-kim@korea.ac.kr. ORCID
  15. Daehyun Baek: School of Biological Sciences, Seoul National University, Seoul, Republic of Korea. baek@snu.ac.kr.
PMID: 34433827 DOI: 10.1038/s41467-021-25361-5

Abstract

COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which infected >200 million people resulting in >4 million deaths. However, temporal landscape of the SARS-CoV-2 translatome and its impact on the human genome remain unexplored. Here, we report a high-resolution atlas of the translatome and transcriptome of SARS-CoV-2 for various time points after infecting human cells. Intriguingly, substantial amount of SARS-CoV-2 translation initiates at a novel translation initiation site (TIS) located in the leader sequence, termed TIS-L. Since TIS-L is included in all the genomic and subgenomic RNAs, the SARS-CoV-2 translatome may be regulated by a sophisticated interplay between TIS-L and downstream TISs. TIS-L functions as a strong translation enhancer for ORF S, and as translation suppressors for most of the other ORFs. Our global temporal atlas provides compelling insight into unique regulation of the SARS-CoV-2 translatome and helps comprehensively evaluate its impact on the human genome.

References

  1. N Engl J Med. 2021 Feb 25;384(8):693-704 [PMID: 32678530]
  2. Trends Biochem Sci. 2003 Apr;28(4):182-8 [PMID: 12713901]
  3. Nat Rev Mol Cell Biol. 2018 Mar;19(3):158-174 [PMID: 29165424]
  4. J Virol. 1991 Jan;65(1):320-5 [PMID: 1985203]
  5. Nature. 2004 Nov 11;432(7014):235-40 [PMID: 15531877]
  6. Annu Rev Virol. 2015 Nov;2(1):265-88 [PMID: 26958916]
  7. Bioinformatics. 2011 Feb 1;27(3):431-2 [PMID: 21149340]
  8. Nature. 2020 Mar;579(7798):270-273 [PMID: 32015507]
  9. Science. 2016 Jan 29;351(6272):aad3867 [PMID: 26823435]
  10. J Virol. 2019 Aug 28;93(18): [PMID: 31243124]
  11. Bioinformatics. 2009 Apr 15;25(8):1091-3 [PMID: 19237447]
  12. Nucleic Acids Res. 2010 Dec;38(22):8328-37 [PMID: 20705652]
  13. Nature. 2004 Nov 11;432(7014):231-5 [PMID: 15531879]
  14. Nat Struct Mol Biol. 2015 May;22(5):404-10 [PMID: 25866880]
  15. Trends Biochem Sci. 1998 Jun;23(6):198-9 [PMID: 9644970]
  16. Mol Cell. 2019 May 2;74(3):494-507.e8 [PMID: 30930054]
  17. N Engl J Med. 2020 Feb 20;382(8):727-733 [PMID: 31978945]
  18. Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5 [PMID: 17130148]
  19. Nat Protoc. 2009;4(1):44-57 [PMID: 19131956]
  20. Nucleic Acids Res. 2021 Jan 8;49(D1):D1144-D1151 [PMID: 33237278]
  21. Nat Genet. 2016 Dec;48(12):1517-1526 [PMID: 27776116]
  22. Cell. 2020 May 14;181(4):914-921.e10 [PMID: 32330414]
  23. Gene Rep. 2020 Jun;19:100682 [PMID: 32300673]
  24. Cell Chem Biol. 2018 Jul 19;25(7):880-890.e3 [PMID: 29754956]
  25. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W70-4 [PMID: 18424795]
  26. J Virol. 2010 Nov;84(21):11418-28 [PMID: 20719948]
  27. Nat Protoc. 2012 Jul 26;7(8):1534-50 [PMID: 22836135]
  28. J Virol. 2007 Jan;81(2):718-31 [PMID: 17079322]
  29. Mol Cell. 2020 Sep 3;79(5):710-727 [PMID: 32853546]
  30. Curr Opin Pharmacol. 2006 Jun;6(3):271-6 [PMID: 16581295]
  31. Genome Biol. 2014;15(12):550 [PMID: 25516281]
  32. Nat Rev Microbiol. 2021 Mar;19(3):155-170 [PMID: 33116300]
  33. Int J Surg. 2020 Jun;78:185-193 [PMID: 32305533]
  34. Cell. 2020 Apr 16;181(2):281-292.e6 [PMID: 32155444]
  35. Nature. 2010 Aug 12;466(7308):835-40 [PMID: 20703300]
  36. Cell. 2011 Nov 11;147(4):789-802 [PMID: 22056041]
  37. Cell. 2006 Jun 2;125(5):887-901 [PMID: 16751099]
  38. Cell. 2013 Feb 14;152(4):844-58 [PMID: 23415231]
  39. Nat Methods. 2015 Feb;12(2):147-53 [PMID: 25486063]
  40. Nat Commun. 2017 Jun 07;8:15730 [PMID: 28589942]
  41. Nat Genet. 2000 May;25(1):25-9 [PMID: 10802651]
  42. Science. 2009 Apr 10;324(5924):218-23 [PMID: 19213877]
  43. Trends Biochem Sci. 2019 Sep;44(9):782-794 [PMID: 31003826]
  44. Nature. 2016 Jul 28;535(7613):570-4 [PMID: 27437580]
  45. Adv Virus Res. 2006;66:193-292 [PMID: 16877062]
  46. J Gen Virol. 2020 Sep;101(9):925-940 [PMID: 32568027]
  47. Cell Rep. 2019 Feb 19;26(8):2126-2139.e9 [PMID: 30784594]
  48. Nucleic Acids Res. 2004 Feb 27;32(4):1382-91 [PMID: 14990743]
  49. RNA. 2012 Jul;18(7):1338-46 [PMID: 22635403]
  50. Cell. 2021 Jan 7;184(1):92-105.e16 [PMID: 33147445]
  51. Viruses. 2021 Jan 14;13(1): [PMID: 33466921]
  52. Mol Cell Biol. 2000 Dec;20(23):8635-42 [PMID: 11073965]
  53. Science. 2012 Jun 29;336(6089):1719-23 [PMID: 22745432]
  54. PLoS Pathog. 2016 Feb 26;12(2):e1005473 [PMID: 26919232]
  55. Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12257-62 [PMID: 20562343]
  56. Nat Biotechnol. 2019 Apr;37(4):420-423 [PMID: 30778233]
  57. Nature. 2021 Jan;589(7840):125-130 [PMID: 32906143]
  58. Immunity. 2019 Apr 16;50(4):907-923 [PMID: 30995506]
  59. Nat Methods. 2012 Mar 04;9(4):357-9 [PMID: 22388286]
  60. J Endocr Soc. 2020 Jul 02;4(8):bvaa082 [PMID: 32728654]
  61. Signal Transduct Target Ther. 2020 Jul 13;5(1):125 [PMID: 32661235]
  62. Bioinformatics. 2013 Jan 1;29(1):15-21 [PMID: 23104886]
  63. Curr Protoc Bioinformatics. 2002 Aug;Chapter 2:Unit 2.3 [PMID: 18792934]
  64. J Virol. 1968 Oct;2(10):955-61 [PMID: 4302013]
  65. Nucleic Acids Res. 2017 Jan 4;45(D1):D482-D490 [PMID: 27899678]
  66. Genes Dev. 2017 Sep 1;31(17):1717-1731 [PMID: 28982758]
  67. Nucleic Acids Res. 2019 Jan 8;47(D1):D419-D426 [PMID: 30407594]
  68. Nucleic Acids Res. 2012 Apr;40(7):2898-906 [PMID: 22156057]
  69. JAMA. 2020 May 12;323(18):1824-1836 [PMID: 32282022]
  70. Cell. 2020 May 28;181(5):1036-1045.e9 [PMID: 32416070]
  71. Nat Rev Endocrinol. 2020 Jul;16(7):363-377 [PMID: 32303708]
  72. Cell. 2020 Apr 16;181(2):271-280.e8 [PMID: 32142651]
  73. Methods Mol Biol. 2015;1282:1-23 [PMID: 25720466]
  74. Nature. 2020 Jul;583(7816):469-472 [PMID: 32408336]
  75. Bioinformatics. 2010 Mar 15;26(6):841-2 [PMID: 20110278]
  76. Nat Rev Immunol. 2020 Jun;20(6):363-374 [PMID: 32346093]
  77. Science. 2020 Aug 7;369(6504):718-724 [PMID: 32661059]
  78. Nature. 2020 Jul;583(7816):459-468 [PMID: 32353859]
  79. Cell. 2020 May 28;181(5):997-1003.e9 [PMID: 32359424]
  80. Translation (Austin). 2013 Apr 01;1(1):e24419 [PMID: 26824019]
  81. Nature. 2020 Mar;579(7798):265-269 [PMID: 32015508]

MeSH Term

COVID-19
Gene Expression Regulation, Viral
Genome, Human
Humans
Open Reading Frames
Protein Biosynthesis
RNA, Viral
SARS-CoV-2
Transcriptome
Viral Proteins

Chemicals

RNA, Viral
Viral Proteins
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

GEN: GEND000446 (A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome)

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