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For: Andreev DE, O'Connor PBF, Fahey C, Kenny EM, Terenin IM, Dmitriev SE, Cormican P, Morris DW, Shatsky IN, Baranov PV. Translation of 5' leaders is pervasive in genes resistant to eIF2 repression. eLife 2015;4:e03971. [PMID: 25621764 PMCID: PMC4383229 DOI: 10.7554/elife.03971] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 01/22/2015] [Indexed: 12/18/2022]  Open
Number Cited by Other Article(s)
201
Liu TY, Huang HH, Wheeler D, Xu Y, Wells JA, Song YS, Wiita AP. Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics. Cell Syst 2017;4:636-644.e9. [PMID: 28578850 DOI: 10.1016/j.cels.2017.05.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/17/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
202
Zhdanov AV, Andreev DE, Baranov PV, Papkovsky DB. Low energy costs of F1Fo ATP synthase reversal in colon carcinoma cells deficient in mitochondrial complex IV. Free Radic Biol Med 2017;106:184-195. [PMID: 28189850 DOI: 10.1016/j.freeradbiomed.2017.02.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/08/2017] [Accepted: 02/08/2017] [Indexed: 10/20/2022]
203
Terenin IM, Smirnova VV, Andreev DE, Dmitriev SE, Shatsky IN. A researcher's guide to the galaxy of IRESs. Cell Mol Life Sci 2017;74:1431-1455. [PMID: 27853833 PMCID: PMC11107752 DOI: 10.1007/s00018-016-2409-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/01/2016] [Accepted: 11/02/2016] [Indexed: 12/25/2022]
204
Sajjanar B, Deb R, Raina SK, Pawar S, Brahmane MP, Nirmale AV, Kurade NP, Manjunathareddy GB, Bal SK, Singh NP. Untranslated regions (UTRs) orchestrate translation reprogramming in cellular stress responses. J Therm Biol 2017;65:69-75. [DOI: 10.1016/j.jtherbio.2017.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 11/29/2022]
205
Gobet C, Naef F. Ribosome profiling and dynamic regulation of translation in mammals. Curr Opin Genet Dev 2017;43:120-127. [PMID: 28363112 DOI: 10.1016/j.gde.2017.03.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 10/19/2022]
206
Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain. PLoS Biol 2017;15:e2001882. [PMID: 28323820 PMCID: PMC5360235 DOI: 10.1371/journal.pbio.2001882] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/22/2017] [Indexed: 01/12/2023]  Open
207
Translation complex profile sequencing to study the in vivo dynamics of mRNA–ribosome interactions during translation initiation, elongation and termination. Nat Protoc 2017;12:697-731. [DOI: 10.1038/nprot.2016.189] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
208
Flavivirus Infection Uncouples Translation Suppression from Cellular Stress Responses. mBio 2017;8:mBio.02150-16. [PMID: 28074025 PMCID: PMC5225315 DOI: 10.1128/mbio.02150-16] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
209
Artcibasova AV, Korzinkin MB, Sorokin MI, Shegay PV, Zhavoronkov AA, Gaifullin N, Alekseev BY, Vorobyev NV, Kuzmin DV, Kaprin АD, Borisov NM, Buzdin AA. MiRImpact, a new bioinformatic method using complete microRNA expression profiles to assess their overall influence on the activity of intracellular molecular pathways. Cell Cycle 2016;15:689-98. [PMID: 27027999 PMCID: PMC4845938 DOI: 10.1080/15384101.2016.1147633] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
210
Rittiner JE, Caffall ZF, Hernández-Martinez R, Sanderson SM, Pearson JL, Tsukayama KK, Liu AY, Xiao C, Tracy S, Shipman MK, Hickey P, Johnson J, Scott B, Stacy M, Saunders-Pullman R, Bressman S, Simonyan K, Sharma N, Ozelius LJ, Cirulli ET, Calakos N. Functional Genomic Analyses of Mendelian and Sporadic Disease Identify Impaired eIF2α Signaling as a Generalizable Mechanism for Dystonia. Neuron 2016;92:1238-1251. [PMID: 27939583 DOI: 10.1016/j.neuron.2016.11.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/27/2016] [Accepted: 11/04/2016] [Indexed: 01/09/2023]
211
Andreev DE, O'Connor PBF, Loughran G, Dmitriev SE, Baranov PV, Shatsky IN. Insights into the mechanisms of eukaryotic translation gained with ribosome profiling. Nucleic Acids Res 2016;45:513-526. [PMID: 27923997 PMCID: PMC5314775 DOI: 10.1093/nar/gkw1190] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/31/2016] [Accepted: 11/18/2016] [Indexed: 12/29/2022]  Open
212
Akulich KA, Andreev DE, Terenin IM, Smirnova VV, Anisimova AS, Makeeva DS, Arkhipova VI, Stolboushkina EA, Garber MB, Prokofjeva MM, Spirin PV, Prassolov VS, Shatsky IN, Dmitriev SE. Four translation initiation pathways employed by the leaderless mRNA in eukaryotes. Sci Rep 2016;6:37905. [PMID: 27892500 PMCID: PMC5124965 DOI: 10.1038/srep37905] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/02/2016] [Indexed: 01/09/2023]  Open
213
The ribosome-engaged landscape of alternative splicing. Nat Struct Mol Biol 2016;23:1117-1123. [PMID: 27820807 DOI: 10.1038/nsmb.3317] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/06/2016] [Indexed: 02/07/2023]
214
Kozel C, Thompson B, Hustak S, Moore C, Nakashima A, Singh CR, Reid M, Cox C, Papadopoulos E, Luna RE, Anderson A, Tagami H, Hiraishi H, Slone EA, Yoshino KI, Asano M, Gillaspie S, Nietfeld J, Perchellet JP, Rothenburg S, Masai H, Wagner G, Beeser A, Kikkawa U, Fleming SD, Asano K. Overexpression of eIF5 or its protein mimic 5MP perturbs eIF2 function and induces ATF4 translation through delayed re-initiation. Nucleic Acids Res 2016;44:8704-8713. [PMID: 27325740 PMCID: PMC5062967 DOI: 10.1093/nar/gkw559] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 11/14/2022]  Open
215
Bal NV, Susorov D, Chesnokova E, Kasianov A, Mikhailova T, Alkalaeva E, Balaban PM, Kolosov P. Upstream Open Reading Frames Located in the Leader of Protein Kinase Mζ mRNA Regulate Its Translation. Front Mol Neurosci 2016;9:103. [PMID: 27790092 PMCID: PMC5061749 DOI: 10.3389/fnmol.2016.00103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/30/2016] [Indexed: 12/17/2022]  Open
216
O'Connor PBF, Andreev DE, Baranov PV. Comparative survey of the relative impact of mRNA features on local ribosome profiling read density. Nat Commun 2016;7:12915. [PMID: 27698342 PMCID: PMC5059445 DOI: 10.1038/ncomms12915] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 08/16/2016] [Indexed: 12/20/2022]  Open
217
Golovko A, Kojukhov A, Guan BJ, Morpurgo B, Merrick WC, Mazumder B, Hatzoglou M, Komar AA. The eIF2A knockout mouse. Cell Cycle 2016;15:3115-3120. [PMID: 27686860 DOI: 10.1080/15384101.2016.1237324] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
218
Gerashchenko MV, Gladyshev VN. Ribonuclease selection for ribosome profiling. Nucleic Acids Res 2016;45:e6. [PMID: 27638886 PMCID: PMC5314788 DOI: 10.1093/nar/gkw822] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/14/2016] [Accepted: 09/06/2016] [Indexed: 11/14/2022]  Open
219
The rules and impact of nonsense-mediated mRNA decay in human cancers. Nat Genet 2016;48:1112-8. [PMID: 27618451 PMCID: PMC5045715 DOI: 10.1038/ng.3664] [Citation(s) in RCA: 339] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/11/2016] [Indexed: 12/19/2022]
220
Curran JA, Weiss B. What Is the Impact of mRNA 5' TL Heterogeneity on Translational Start Site Selection and the Mammalian Cellular Phenotype? Front Genet 2016;7:156. [PMID: 27630668 PMCID: PMC5005323 DOI: 10.3389/fgene.2016.00156] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/16/2016] [Indexed: 12/23/2022]  Open
221
Response of Three Different Viruses to Interferon Priming and Dithiothreitol Treatment of Avian Cells. J Virol 2016;90:8328-40. [PMID: 27440902 DOI: 10.1128/jvi.01175-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 06/30/2016] [Indexed: 02/05/2023]  Open
222
Ribosome Footprint Profiling of Translation throughout the Genome. Cell 2016;165:22-33. [PMID: 27015305 DOI: 10.1016/j.cell.2016.02.066] [Citation(s) in RCA: 294] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 12/15/2022]
223
Bercovich-Kinori A, Tai J, Gelbart IA, Shitrit A, Ben-Moshe S, Drori Y, Itzkovitz S, Mandelboim M, Stern-Ginossar N. A systematic view on influenza induced host shutoff. eLife 2016;5. [PMID: 27525483 PMCID: PMC5028189 DOI: 10.7554/elife.18311] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/14/2016] [Indexed: 12/25/2022]  Open
224
Cabrera-Quio LE, Herberg S, Pauli A. Decoding sORF translation - from small proteins to gene regulation. RNA Biol 2016;13:1051-1059. [PMID: 27653973 DOI: 10.1080/15476286.2016.1218589] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
225
Young SK, Wek RC. Upstream Open Reading Frames Differentially Regulate Gene-specific Translation in the Integrated Stress Response. J Biol Chem 2016;291:16927-35. [PMID: 27358398 DOI: 10.1074/jbc.r116.733899] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
226
Hinnebusch AG, Ivanov IP, Sonenberg N. Translational control by 5'-untranslated regions of eukaryotic mRNAs. Science 2016;352:1413-6. [PMID: 27313038 DOI: 10.1126/science.aad9868] [Citation(s) in RCA: 748] [Impact Index Per Article: 83.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
227
Gamil AAA, Xu C, Mutoloki S, Evensen Ø. PKR Activation Favors Infectious Pancreatic Necrosis Virus Replication in Infected Cells. Viruses 2016;8:v8060173. [PMID: 27338445 PMCID: PMC4926193 DOI: 10.3390/v8060173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/31/2016] [Accepted: 06/03/2016] [Indexed: 01/17/2023]  Open
228
Complementary Roles of GADD34- and CReP-Containing Eukaryotic Initiation Factor 2α Phosphatases during the Unfolded Protein Response. Mol Cell Biol 2016;36:1868-80. [PMID: 27161320 DOI: 10.1128/mcb.00190-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 04/27/2016] [Indexed: 02/02/2023]  Open
229
Steffen KK, Dillin A. A Ribosomal Perspective on Proteostasis and Aging. Cell Metab 2016;23:1004-1012. [PMID: 27304502 DOI: 10.1016/j.cmet.2016.05.013] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/23/2016] [Accepted: 05/26/2016] [Indexed: 12/31/2022]
230
Tzani I, Ivanov IP, Andreev DE, Dmitriev RI, Dean KA, Baranov PV, Atkins JF, Loughran G. Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform. Open Biol 2016;6:rsob.150203. [PMID: 27249819 PMCID: PMC4892431 DOI: 10.1098/rsob.150203] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/26/2016] [Indexed: 12/22/2022]  Open
231
Chew GL, Pauli A, Schier AF. Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish. Nat Commun 2016;7:11663. [PMID: 27216465 PMCID: PMC4890304 DOI: 10.1038/ncomms11663] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 04/18/2016] [Indexed: 02/07/2023]  Open
232
Zhang L, Hapon MB, Goyeneche AA, Srinivasan R, Gamarra-Luques CD, Callegari EA, Drappeau DD, Terpstra EJ, Pan B, Knapp JR, Chien J, Wang X, Eyster KM, Telleria CM. Mifepristone increases mRNA translation rate, triggers the unfolded protein response, increases autophagic flux, and kills ovarian cancer cells in combination with proteasome or lysosome inhibitors. Mol Oncol 2016;10:1099-117. [PMID: 27233943 DOI: 10.1016/j.molonc.2016.05.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/25/2016] [Accepted: 05/11/2016] [Indexed: 12/12/2022]  Open
233
Diament A, Tuller T. Estimation of ribosome profiling performance and reproducibility at various levels of resolution. Biol Direct 2016;11:24. [PMID: 27160013 PMCID: PMC4862193 DOI: 10.1186/s13062-016-0127-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/29/2016] [Indexed: 01/23/2023]  Open
234
Wang C, Han B, Zhou R, Zhuang X. Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells. Cell 2016;165:990-1001. [PMID: 27153499 PMCID: PMC4905760 DOI: 10.1016/j.cell.2016.04.040] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/07/2016] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
235
Truitt ML, Ruggero D. New frontiers in translational control of the cancer genome. Nat Rev Cancer 2016;16:288-304. [PMID: 27112207 PMCID: PMC5491099 DOI: 10.1038/nrc.2016.27] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
236
Fields AP, Rodriguez EH, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, Weissman JS. A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation. Mol Cell 2016;60:816-827. [PMID: 26638175 PMCID: PMC4720255 DOI: 10.1016/j.molcel.2015.11.013] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/08/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
237
Ma J, Diedrich JK, Jungreis I, Donaldson C, Vaughan J, Kellis M, Yates JR, Saghatelian A. Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides. Anal Chem 2016;88:3967-75. [PMID: 27010111 DOI: 10.1021/acs.analchem.6b00191] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
238
Terenin IM, Akulich KA, Andreev DE, Polyanskaya SA, Shatsky IN, Dmitriev SE. Sliding of a 43S ribosomal complex from the recognized AUG codon triggered by a delay in eIF2-bound GTP hydrolysis. Nucleic Acids Res 2016;44:1882-93. [PMID: 26717981 PMCID: PMC4770231 DOI: 10.1093/nar/gkv1514] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 02/05/2023]  Open
239
Johnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. EMBO J 2016;35:706-23. [PMID: 26896445 DOI: 10.15252/embj.201592759] [Citation(s) in RCA: 259] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/08/2016] [Indexed: 12/20/2022]  Open
240
Starck SR, Tsai JC, Chen K, Shodiya M, Wang L, Yahiro K, Martins-Green M, Shastri N, Walter P. Translation from the 5' untranslated region shapes the integrated stress response. Science 2016;351:aad3867. [PMID: 26823435 DOI: 10.1126/science.aad3867] [Citation(s) in RCA: 274] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
241
Sheshukova EV, Shindyapina AV, Komarova TV, Dorokhov YL. “Matreshka” genes with alternative reading frames. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
242
Michel AM, Mullan JPA, Velayudhan V, O'Connor PBF, Donohue CA, Baranov PV. RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data. RNA Biol 2016;13:316-9. [PMID: 26821742 PMCID: PMC4829337 DOI: 10.1080/15476286.2016.1141862] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
243
Mouilleron H, Delcourt V, Roucou X. Death of a dogma: eukaryotic mRNAs can code for more than one protein. Nucleic Acids Res 2016;44:14-23. [PMID: 26578573 PMCID: PMC4705651 DOI: 10.1093/nar/gkv1218] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/13/2022]  Open
244
Detecting actively translated open reading frames in ribosome profiling data. Nat Methods 2015;13:165-70. [PMID: 26657557 DOI: 10.1038/nmeth.3688] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/28/2015] [Indexed: 12/23/2022]
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Reid DW, Shenolikar S, Nicchitta CV. Simple and inexpensive ribosome profiling analysis of mRNA translation. Methods 2015;91:69-74. [PMID: 26164698 PMCID: PMC4684803 DOI: 10.1016/j.ymeth.2015.07.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/22/2015] [Accepted: 07/06/2015] [Indexed: 12/14/2022]  Open
246
Dieudonné FX, O'Connor PBF, Gubler-Jaquier P, Yasrebi H, Conne B, Nikolaev S, Antonarakis S, Baranov PV, Curran J. The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype. BMC Genomics 2015;16:986. [PMID: 26589636 PMCID: PMC4654819 DOI: 10.1186/s12864-015-2179-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/31/2015] [Indexed: 11/10/2022]  Open
247
Ribosome profiling reveals the what, when, where and how of protein synthesis. Nat Rev Mol Cell Biol 2015;16:651-64. [PMID: 26465719 DOI: 10.1038/nrm4069] [Citation(s) in RCA: 362] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
248
Young SK, Willy JA, Wu C, Sachs MS, Wek RC. Ribosome Reinitiation Directs Gene-specific Translation and Regulates the Integrated Stress Response. J Biol Chem 2015;290:28257-28271. [PMID: 26446796 DOI: 10.1074/jbc.m115.693184] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Indexed: 12/24/2022]  Open
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Legrand N, Jaquier-Gubler P, Curran J. The impact of the phosphomimetic eIF2αS/D on global translation, reinitiation and the integrated stress response is attenuated in N2a cells. Nucleic Acids Res 2015;43:8392-404. [PMID: 26264663 PMCID: PMC4787802 DOI: 10.1093/nar/gkv827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/04/2015] [Indexed: 12/21/2022]  Open
250
Stern-Ginossar N, Ingolia NT. Ribosome Profiling as a Tool to Decipher Viral Complexity. Annu Rev Virol 2015;2:335-49. [PMID: 26958919 DOI: 10.1146/annurev-virology-100114-054854] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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