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For: Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 2009;324:218-23. [PMID: 19213877 DOI: 10.1126/science.1168978] [Citation(s) in RCA: 2836] [Impact Index Per Article: 177.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Number Cited by Other Article(s)
151
Ramalho S, Dopler A, Faller W. Ribosome specialization in cancer: a spotlight on ribosomal proteins. NAR Cancer 2024;6:zcae029. [PMID: 38989007 PMCID: PMC11231584 DOI: 10.1093/narcan/zcae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024]  Open
152
Peyretaillade E, Akossi RF, Tournayre J, Delbac F, Wawrzyniak I. How to overcome constraints imposed by microsporidian genome features to ensure gene prediction? J Eukaryot Microbiol 2024;71:e13038. [PMID: 38934348 DOI: 10.1111/jeu.13038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
153
Mangkalaphiban K, Ganesan R, Jacobson A. Pleiotropic effects of PAB1 deletion: Extensive changes in the yeast proteome, transcriptome, and translatome. PLoS Genet 2024;20:e1011392. [PMID: 39236083 PMCID: PMC11407637 DOI: 10.1371/journal.pgen.1011392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 09/17/2024] [Accepted: 08/11/2024] [Indexed: 09/07/2024]  Open
154
Miao B, Ge L, He C, Wang X, Wu J, Li X, Chen K, Wan J, Xing S, Ren L, Shi Z, Liu S, Hu Y, Chen J, Yu Y, Feng L, Flores NM, Liang Z, Xu X, Wang R, Zhou J, Fan J, Xiang B, Li E, Mao Y, Cheng J, Zhao K, Mazur PK, Cai J, Lan F. SMYD5 is a ribosomal methyltransferase that catalyzes RPL40 lysine methylation to enhance translation output and promote hepatocellular carcinoma. Cell Res 2024;34:648-660. [PMID: 39103523 PMCID: PMC11369092 DOI: 10.1038/s41422-024-01013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 07/23/2024] [Indexed: 08/07/2024]  Open
155
Nor Amdan NA, Shahrulzamri NA, Hashim R, Mohamad Jamil N. Understanding the evolution of macrolides resistance: A mini review. J Glob Antimicrob Resist 2024;38:368-375. [PMID: 39117142 DOI: 10.1016/j.jgar.2024.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 05/31/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024]  Open
156
Feidantsis K, Panteli N, Bousdras T, Gai F, Gasco L, Antonopoulou E. Dietary Tenebrio molitor larvae meal effects on cellular stress responses, antioxidant status and intermediate metabolism of Oncorhynchus mykiss. J Anim Physiol Anim Nutr (Berl) 2024;108:1270-1285. [PMID: 38657021 DOI: 10.1111/jpn.13970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
157
Lyons EF, Devanneaux LC, Muller RY, Freitas AV, Meacham ZA, McSharry MV, Trinh VN, Rogers AJ, Ingolia NT, Lareau LF. Translation elongation as a rate limiting step of protein production. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.27.568910. [PMID: 38076849 PMCID: PMC10705293 DOI: 10.1101/2023.11.27.568910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
158
Liu J, Zhong B, Li S, Han S. Mapping subcellular RNA localization with proximity labeling. Acta Biochim Biophys Sin (Shanghai) 2024;57:101-107. [PMID: 39210826 PMCID: PMC11802345 DOI: 10.3724/abbs.2024147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]  Open
159
Ma J, Zhang L, Zhang X, Zhang L, Zhang H, Zhu Y, Huang X, Zhang T, Tang X, Wang Y, Chen L, Pu Q, Yang L, Cao Z, Ding BS. Inhibiting endothelial Rhoj blocks profibrotic vascular intussusception and angiocrine factors to sustain lung regeneration. Sci Transl Med 2024;16:eado5266. [PMID: 39196961 DOI: 10.1126/scitranslmed.ado5266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 08/07/2024] [Indexed: 08/30/2024]
160
Kumar R, Zhang F, Niphadkar S, Onu C, Vijjamarri AK, Greenberg ML, Laxman S, Hinnebusch AG. Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in post-transcriptional repression of starvation-induced pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.610059. [PMID: 39257769 PMCID: PMC11383670 DOI: 10.1101/2024.08.28.610059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
161
Fu G, Luo H, Jia J, Hou M, Hu G. Translational Regulation of Duplicated Gene Expression Evolution in Allopolyploid Cotton. Genes (Basel) 2024;15:1130. [PMID: 39336721 PMCID: PMC11431062 DOI: 10.3390/genes15091130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/30/2024]  Open
162
Tresky R, Miyamoto Y, Nagayoshi Y, Yabuki Y, Araki K, Takahashi Y, Komohara Y, Ge H, Nishiguchi K, Fukuda T, Kaneko H, Maeda N, Matsuura J, Iwasaki S, Sakakida K, Shioda N, Wei FY, Tomizawa K, Chujo T. TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice. Nucleic Acids Res 2024;52:9230-9246. [PMID: 38950903 PMCID: PMC11347157 DOI: 10.1093/nar/gkae520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 05/09/2024] [Accepted: 06/04/2024] [Indexed: 07/03/2024]  Open
163
Artimagnella O, Maftei ES, Esposito M, Sanges R, Mallamaci A. Foxg1 regulates translation of neocortical neuronal genes, including the main NMDA receptor subunit gene, Grin1. BMC Biol 2024;22:180. [PMID: 39183266 PMCID: PMC11346056 DOI: 10.1186/s12915-024-01979-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/12/2024] [Indexed: 08/27/2024]  Open
164
Tomuro K, Mito M, Toh H, Kawamoto N, Miyake T, Chow SYA, Doi M, Ikeuchi Y, Shichino Y, Iwasaki S. Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts. Nat Commun 2024;15:7061. [PMID: 39187487 PMCID: PMC11347596 DOI: 10.1038/s41467-024-51258-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/02/2024] [Indexed: 08/28/2024]  Open
165
No EG, Blank HM, Polymenis M. Patterns of protein synthesis in the budding yeast cell cycle: variable or constant? MICROBIAL CELL (GRAZ, AUSTRIA) 2024;11:321-327. [PMID: 39188509 PMCID: PMC11345583 DOI: 10.15698/mic2024.08.835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/06/2024] [Accepted: 08/09/2024] [Indexed: 08/28/2024]
166
Schlusser N, González A, Pandey M, Zavolan M. Current limitations in predicting mRNA translation with deep learning models. Genome Biol 2024;25:227. [PMID: 39164757 PMCID: PMC11337900 DOI: 10.1186/s13059-024-03369-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 08/07/2024] [Indexed: 08/22/2024]  Open
167
Gong X, Liu Y, Wu G, Xu Z, Zeng L, Tian M, Zhang R, Zeng C, Chen Y. An updated resource for the detection of protein-coding circRNA with CircProPlus. Sci Rep 2024;14:19040. [PMID: 39152148 PMCID: PMC11329775 DOI: 10.1038/s41598-024-69744-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024]  Open
168
Ortega Moreno L, Chaparro M, Gisbert JP. Long Non-Coding RNAs and Their Potential Role as Biomarkers in Inflammatory Bowel Disease. Int J Mol Sci 2024;25:8808. [PMID: 39201494 PMCID: PMC11354568 DOI: 10.3390/ijms25168808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024]  Open
169
Verheyden NA, Klostermann M, Brüggemann M, Steede H, Scholz A, Amr S, Lichtenthaeler C, Münch C, Schmid T, Zarnack K, Krueger A. A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match. Nucleic Acids Res 2024;52:8515-8533. [PMID: 38783381 PMCID: PMC11317165 DOI: 10.1093/nar/gkae416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]  Open
170
Zhang Y. LncRNA-encoded peptides in cancer. J Hematol Oncol 2024;17:66. [PMID: 39135098 PMCID: PMC11320871 DOI: 10.1186/s13045-024-01591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]  Open
171
Vieira de Souza E, L Bookout A, Barnes CA, Miller B, Machado P, Basso LA, Bizarro CV, Saghatelian A. Rp3: Ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery. Nat Commun 2024;15:6839. [PMID: 39122697 PMCID: PMC11316118 DOI: 10.1038/s41467-024-50301-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 07/08/2024] [Indexed: 08/12/2024]  Open
172
Roiuk M, Neff M, Teleman AA. eIF4E-independent translation is largely eIF3d-dependent. Nat Commun 2024;15:6692. [PMID: 39107322 PMCID: PMC11303786 DOI: 10.1038/s41467-024-51027-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 07/22/2024] [Indexed: 08/10/2024]  Open
173
Ding S, Liao H, Huang F, Chen L, Guo W, Feng K, Huang T, Cai YD. Analyzing domain features of small proteins using a machine-learning method. Proteomics 2024;24:e2300302. [PMID: 38258387 DOI: 10.1002/pmic.202300302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
174
Yang H, Thompson B. Widespread changes to the translational landscape in a maize microRNA biogenesis mutant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024;119:1986-2000. [PMID: 38963711 DOI: 10.1111/tpj.16902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 06/08/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
175
Schultz SK, Kothe U. RNA modifying enzymes shape tRNA biogenesis and function. J Biol Chem 2024;300:107488. [PMID: 38908752 PMCID: PMC11301382 DOI: 10.1016/j.jbc.2024.107488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024]  Open
176
Nugent PJ, Park H, Wladyka CL, Chen KY, Bynum C, Quarterman G, Hsieh AC, Subramaniam AR. Decoding RNA Metabolism by RNA-linked CRISPR Screening in Human Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.25.605204. [PMID: 39091804 PMCID: PMC11291135 DOI: 10.1101/2024.07.25.605204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
177
Perdikopanis N, Giannakakis A, Kavakiotis I, Hatzigeorgiou AG. D-sORF: Accurate Ab Initio Classification of Experimentally Detected Small Open Reading Frames (sORFs) Associated with Translational Machinery. BIOLOGY 2024;13:563. [PMID: 39194501 DOI: 10.3390/biology13080563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024]
178
Ge A, Chan C, Yang X. Exploring the Dark Matter of Human Proteome: The Emerging Role of Non-Canonical Open Reading Frame (ncORF) in Cancer Diagnosis, Biology, and Therapy. Cancers (Basel) 2024;16:2660. [PMID: 39123386 PMCID: PMC11311765 DOI: 10.3390/cancers16152660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]  Open
179
Xie Y, Shu T, Liu T, Spindler MC, Mahamid J, Hocky GM, Gresham D, Holt LJ. Polysome collapse and RNA condensation fluidize the cytoplasm. Mol Cell 2024;84:2698-2716.e9. [PMID: 39059370 PMCID: PMC11539954 DOI: 10.1016/j.molcel.2024.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 03/25/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024]
180
Duenas MA, Craig RJ, Gallaher SD, Moseley JL, Merchant SS. Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.605010. [PMID: 39091764 PMCID: PMC11291117 DOI: 10.1101/2024.07.24.605010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
181
Zhao J, Huang Y, Liukang C, Yang R, Tang L, Sun L, Zhao Y, Zhang G. Dissecting infectious bronchitis virus-induced host shutoff at the translation level. J Virol 2024;98:e0083024. [PMID: 38940559 PMCID: PMC11265393 DOI: 10.1128/jvi.00830-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/01/2024] [Indexed: 06/29/2024]  Open
182
Horvath A, Janapala Y, Woodward K, Mahmud S, Cleynen A, Gardiner E, Hannan R, Eyras E, Preiss T, Shirokikh N. Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress. Nucleic Acids Res 2024;52:7925-7946. [PMID: 38721779 PMCID: PMC11260467 DOI: 10.1093/nar/gkae365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/21/2024] [Accepted: 04/25/2024] [Indexed: 07/23/2024]  Open
183
Dutcher HA, Gasch AP. Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604323. [PMID: 39091809 PMCID: PMC11291059 DOI: 10.1101/2024.07.19.604323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
184
Hou M, Fan W, Zhong D, Dai X, Wang Q, Liu W, Li S. Ribosome Pausing Negatively Regulates Protein Translation in Maize Seedlings during Dark-to-Light Transitions. Int J Mol Sci 2024;25:7985. [PMID: 39063227 PMCID: PMC11277263 DOI: 10.3390/ijms25147985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024]  Open
185
Ichinose T, Kondo S, Kanno M, Shichino Y, Mito M, Iwasaki S, Tanimoto H. Translational regulation enhances distinction of cell types in the nervous system. eLife 2024;12:RP90713. [PMID: 39010741 PMCID: PMC11251722 DOI: 10.7554/elife.90713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]  Open
186
Komar AA, Samatova E, Rodnina MV. Translation Rates and Protein Folding. J Mol Biol 2024;436:168384. [PMID: 38065274 DOI: 10.1016/j.jmb.2023.168384] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023]
187
Dea A, Pincus D. The Heat Shock Response as a Condensate Cascade. J Mol Biol 2024;436:168642. [PMID: 38848866 PMCID: PMC11214683 DOI: 10.1016/j.jmb.2024.168642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
188
Sejour R, Leatherwood J, Yurovsky A, Futcher B. Enrichment of rare codons at 5' ends of genes is a spandrel caused by evolutionary sequence turnover and does not improve translation. eLife 2024;12:RP89656. [PMID: 39008347 PMCID: PMC11249729 DOI: 10.7554/elife.89656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]  Open
189
Camarena ME, Theunissen P, Ruiz M, Ruiz-Orera J, Calvo-Serra B, Castelo R, Castro C, Sarobe P, Fortes P, Perera-Bel J, Albà MM. Microproteins encoded by noncanonical ORFs are a major source of tumor-specific antigens in a liver cancer patient meta-cohort. SCIENCE ADVANCES 2024;10:eadn3628. [PMID: 38985879 PMCID: PMC11235171 DOI: 10.1126/sciadv.adn3628] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
190
Chen M, Dai S, Chen D, Chen H, Feng N, Zheng D. Unveiling the translational dynamics of lychee (Litchi chinesis Sonn.) in response to cold stress. BMC Genomics 2024;25:686. [PMID: 38992605 PMCID: PMC11241792 DOI: 10.1186/s12864-024-10591-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 07/03/2024] [Indexed: 07/13/2024]  Open
191
Weber R, Chang CT. Human DDX6 regulates translation and decay of inefficiently translated mRNAs. eLife 2024;13:RP92426. [PMID: 38989862 PMCID: PMC11239181 DOI: 10.7554/elife.92426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]  Open
192
Roshan P, Biswas A, Anagnos S, Luebbers R, Harish K, Ahmed S, Li M, Nguyen N, Zhou G, Tedeschi F, Hathuc V, Lin Z, Hamilton Z, Origanti S. Modulation of ribosomal subunit associations by eIF6 is critical for mitotic exit and cancer progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600220. [PMID: 38979253 PMCID: PMC11230244 DOI: 10.1101/2024.06.24.600220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
193
Spealman P, de Santana C, De T, Gresham D. Multilevel gene expression changes in lineages containing adaptive copy number variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.20.563336. [PMID: 37961325 PMCID: PMC10634702 DOI: 10.1101/2023.10.20.563336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
194
Rich A, Acar O, Carvunis AR. Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome. Genome Biol 2024;25:183. [PMID: 38978079 PMCID: PMC11232214 DOI: 10.1186/s13059-024-03287-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 05/20/2024] [Indexed: 07/10/2024]  Open
195
Fu Y, Jiang F, Zhang X, Pan Y, Xu R, Liang X, Wu X, Li X, Lin K, Shi R, Zhang X, Ferrandon D, Liu J, Pei D, Wang J, Wang T. Perturbation of METTL1-mediated tRNA N7- methylguanosine modification induces senescence and aging. Nat Commun 2024;15:5713. [PMID: 38977661 PMCID: PMC11231295 DOI: 10.1038/s41467-024-49796-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 06/14/2024] [Indexed: 07/10/2024]  Open
196
Vara C, Montañés JC, Albà MM. High Polymorphism Levels of De Novo ORFs in a Yoruba Human Population. Genome Biol Evol 2024;16:evae126. [PMID: 38934859 PMCID: PMC11221430 DOI: 10.1093/gbe/evae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/08/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024]  Open
197
Sainz MM, Sotelo-Silveira M, Filippi CV, Zardo S. Legume-rhizobia symbiosis: Translatome analysis. Genet Mol Biol 2024;47Suppl 1:e20230284. [PMID: 38954532 PMCID: PMC11223499 DOI: 10.1590/1678-4685-gmb-2023-0284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/31/2024] [Indexed: 07/04/2024]  Open
198
Ross SJ, Hume AJ, Olejnik J, Turcinovic J, Honko AN, McKay LGA, Connor JH, Griffiths A, Mühlberger E, Cifuentes D. Low-Input, High-Resolution 5' Terminal Filovirus RNA Sequencing with ViBE-Seq. Viruses 2024;16:1064. [PMID: 39066227 PMCID: PMC11281615 DOI: 10.3390/v16071064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/14/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024]  Open
199
Wu X, Yuan H, Wu Q, Gao Y, Duan T, Yang K, Huang T, Wang S, Yuan F, Lee D, Taori S, Plute T, Heissel S, Alwaseem H, Isay-Del Viscio M, Molina H, Agnihotri S, Hsu DJ, Zhang N, Rich JN. Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming. NATURE CANCER 2024;5:1024-1044. [PMID: 38519786 PMCID: PMC11552442 DOI: 10.1038/s43018-024-00748-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/23/2024] [Indexed: 03/25/2024]
200
Fernandez SG, Ferguson L, Ingolia NT. Ribosome rescue factor PELOTA modulates translation start site choice for C/EBPα protein isoforms. Life Sci Alliance 2024;7:e202302501. [PMID: 38803235 PMCID: PMC11109482 DOI: 10.26508/lsa.202302501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024]  Open
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