Decoding viral infection by ribosome profiling

Journal of Virology

Volumn 89, Issue 12, 2015, Pages 6164-6166

  Stern Ginossar, Noam ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; VIRUS RNA;

ARTICLE; GENE EXPRESSION; GENETIC TRANSCRIPTION; HOST RESISTANCE; HUMAN; HUMAN CYTOMEGALOVIRUS; HUMAN HERPESVIRUS 8; OPEN READING FRAME; PRIORITY JOURNAL; RIBOSOME; RNA STABILITY; RNA TRANSLATION; VIRUS CELL INTERACTION; VIRUS GENOME; VIRUS INFECTION; VIRUS INFECTIVITY; VIRUS REPLICATION; CYTOMEGALOVIRUS; CYTOMEGALOVIRUS INFECTION; GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; HERPES VIRUS INFECTION; MOLECULAR BIOLOGY; PROCEDURES; PROTEIN SYNTHESIS; VIROLOGY;

HUMAN HERPESVIRUS 5; HUMAN HERPESVIRUS 8;

CYTOMEGALOVIRUS; CYTOMEGALOVIRUS INFECTIONS; GENE EXPRESSION PROFILING; HERPESVIRIDAE INFECTIONS; HERPESVIRUS 8, HUMAN; HUMANS; MOLECULAR BIOLOGY; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, MESSENGER;

EID: 84929598198     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.02528-14     Document Type: Article

References (20)

1. Ingolia NT, Lareau LF, Weissman JS. 2011. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147:789-802. http://dx.doi.org/10.1016/j.cell.2011.10.002.
2. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genomewide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-223. http://dx.doi.org/10.1126/science.1168978.
3. Steitz JA. 1969. Polypeptide chain initiation: nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA. Nature 224:957-964. http://dx.doi.org/10.1038/224957a0.
4. Wolin SL, Walter P. 1988. Ribosome pausing and stacking during translation of a eukaryotic mRNA. EMBO J 7:3559-3569.
5. Jeudy S, Abergel C, Claverie J-M, Legendre M. 2012. Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes. PLoS Genet 8:e1003122. http://dx.doi.org/10.1371/journal.pgen.1003122.
6. Firth AE, Brierley I. 2012. Non-canonical translation in RNA viruses. J Gen Virol 93:1385-1409. http://dx.doi.org/10.1099/vir.0.042499-0.
7. Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H, Mann M, Ingolia NT, Weissman JS. 2012. Decoding human cytomegalovirus. Science 338:1088-1093. http://dx.doi.org/10.1126/science.1227919.
8. Arias C, Weisburd B, Stern-Ginossar N, Mercier A, Madrid AS, Bellare P, Holdorf M, Weissman JS, Ganem D. 2014. KSHV 2.0: a comprehensive annotation of the Kaposi's sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features. PLoS Pathog 10:e1003847. http://dx.doi.org/10.1371/journal.ppat.1003847.
9. Andrews SJ, Rothnagel JA. 2014. Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet 15:193-204. http://dx.doi.org/10.1038/nrg3520.
10. Ladoukakis E, Pereira V, Magny EG, Eyre-Walker A, Couso JP. 2011. Hundreds of putatively functional small open reading frames in Drosophila. Genome Biol 12:R118. http://dx.doi.org/10.1186/gb-2011-12-11-r118.
11. Barbosa C, Peixeiro I, Romão L. 2013. Gene expression regulation by upstream open reading frames and human disease. PLoS Genet 9:e1003529. http://dx.doi.org/10.1371/journal.pgen.1003529.
12. Dunn JG, Foo CK, Belletier NG, Gavis ER, Weissman JS. 2013. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. eLife 2:e01179. http://dx.doi.org/10.7554/eLife.01179.
13. Yewdell JW. 2007. Plumbing the sources of endogenous MHC class I peptide ligands. Curr Opin Immunol 19:79-86. http://dx.doi.org/10.1016/j.coi.2006.11.010.
14. Sylwester AW, Mitchell BL, Edgar JB, Taormina C, Pelte C, Ruchti F, Sleath PR, Grabstein KH, Hosken NA, Kern F, Nelson JA, Picker LJ. 2005. Broadly targeted human cytomegalovirus-specific CD4+ and CD8+ T cells dominate the memory compartments of exposed subjects. J Exp Med 202:673-685. http://dx.doi.org/10.1084/jem.20050882.
15. Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJ, Jackson SE, Wills MR, Weissman JS. 2014. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep 8:1365-1379. http://dx.doi.org/10.1016/j.celrep.2014.07.045.
16. Chambers J, Angulo A, Amaratunga D, Guo H, Jiang Y, Wan JS, Bittner A, Frueh K, Jackson MR, Peterson PA, Erlander MG, Ghazal P. 1999. DNA microarrays of the complex human cytomegalovirus genome: profiling kinetic class with drug sensitivity of viral gene expression. J Virol 73:5757-5766.
17. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL. 2002. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci USA 99:15687-15692. http://dx.doi.org/10.1073/pnas.242579699.
18. Weekes MP, Tomasec P, Huttlin EL, Fielding CA, Nusinow D, Stanton RJ, Wang ECY, Aicheler R, Murrell I, Wilkinson GW, Lehner PJ, Gygi SP. 2014. Quantitative temporal viromics: an approach to investigate hostpathogen interaction. Cell 157:1460-1472. http://dx.doi.org/10.1016/j.cell.2014.04.028.
19. Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chainterminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467. http://dx.doi.org/10.1073/pnas.74.12.5463.
20. Fiers W, Contreras R, Haegemann G, Rogiers R, Van de Voorde A, Van Heuverswyn H, Van Herreweghe J, Volckaert G, Ysebaert M. 1978. Complete nucleotide sequence of SV40 DNA. Nature 273:113-120. http://dx.doi.org/10.1038/273113a0.