{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T10:10:17Z","timestamp":1765966217598,"version":"3.48.0"},"reference-count":208,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T00:00:00Z","timestamp":1765929600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T00:00:00Z","timestamp":1765929600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"DOI":"10.1038\/s42003-025-09156-8","type":"journal-article","created":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T10:02:34Z","timestamp":1765965754000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia"],"prefix":"10.1038","volume":"8","author":[{"given":"Elissa","family":"Khadra","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zoaila","family":"Iqbal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4935-7065","authenticated-orcid":false,"given":"Morgane","family":"Le Gall","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guilhem","family":"Clary","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francoise","family":"Levavasseur","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zubaidan","family":"Tuerdi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0646-0617","authenticated-orcid":false,"given":"Charles","family":"Dussiau","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8910-0945","authenticated-orcid":false,"given":"David","family":"Rombaut","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5247-8976","authenticated-orcid":false,"given":"Marie","family":"Temple","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8640-9776","authenticated-orcid":false,"given":"Chloe","family":"Friedrich","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Romain","family":"Vazquez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Justine","family":"Decroocq","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cl\u00e9ment","family":"Larrue","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Didier","family":"Bouscary","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6021-4057","authenticated-orcid":false,"given":"Olivier","family":"Kosmider","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0601-3948","authenticated-orcid":false,"given":"Nicolas","family":"Chapuis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yannick","family":"Simoni","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0167-5996","authenticated-orcid":false,"given":"Jerome","family":"Tamburini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Evelyne","family":"Lauret","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michaela","family":"Fontenay","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rudy","family":"Birsen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emilie-Fleur","family":"Gautier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1839-8411","authenticated-orcid":false,"given":"Ismael","family":"Boussaid","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,12,17]]},"reference":[{"key":"9156_CR1","doi-asserted-by":"publisher","first-page":"1265","DOI":"10.1016\/j.cell.2019.01.031","volume":"176","author":"P van Galen","year":"2019","unstructured":"van Galen, P. et al. Single-cell RNA-Seq reveals AML hierarchies relevant to disease progression and immunity. Cell 176, 1265\u20131281.e24 (2019).","journal-title":"Cell"},{"key":"9156_CR2","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1038\/s41375-024-02137-6","volume":"38","author":"JF Severens","year":"2024","unstructured":"Severens, J. F. et al. Mapping AML heterogeneity - multi-cohort transcriptomic analysis identifies novel clusters and divergent ex-vivo drug responses. Leukemia 38, 751\u2013761 (2024).","journal-title":"Leukemia"},{"key":"9156_CR3","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aax2863","volume":"11","author":"D Sharon","year":"2019","unstructured":"Sharon, D. et al. Inhibition of mitochondrial translation overcomes venetoclax resistance in AML through activation of the integrated stress response. Sci. Transl. Med. 11, eaax2863 (2019).","journal-title":"Sci. Transl. Med."},{"key":"9156_CR4","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1016\/j.ccell.2018.01.012","volume":"33","author":"T Yamauchi","year":"2018","unstructured":"Yamauchi, T. et al. Genome-wide CRISPR-Cas9 screen identifies leukemia-specific dependence on a Pre-mRNA metabolic pathway regulated by DCPS. Cancer Cell 33, 386\u2013400.e5 (2018).","journal-title":"Cancer Cell"},{"key":"9156_CR5","doi-asserted-by":"publisher","first-page":"1107","DOI":"10.1016\/j.molcel.2022.02.025","volume":"82","author":"G Biancon","year":"2022","unstructured":"Biancon, G. et al. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Mol. Cell 82, 1107\u20131122.e7 (2022).","journal-title":"Mol. Cell"},{"key":"9156_CR6","doi-asserted-by":"publisher","unstructured":"Kodali, S. et al. RNA sequestration in P-bodies sustains myeloid leukaemia. Nat. Cell Biol. 1\u201314 https:\/\/doi.org\/10.1038\/s41556-024-01489-6 (2024).","DOI":"10.1038\/s41556-024-01489-6"},{"key":"9156_CR7","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/j.ccell.2019.01.010","volume":"35","author":"E Wang","year":"2019","unstructured":"Wang, E. et al. Targeting an RNA-binding protein network in acute myeloid leukemia. Cancer Cell 35, 369\u2013384.e7 (2019).","journal-title":"Cancer Cell"},{"key":"9156_CR8","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1038\/nature24678","volume":"552","author":"I Barbieri","year":"2017","unstructured":"Barbieri, I. et al. Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control. Nature 552, 126\u2013131 (2017).","journal-title":"Nature"},{"key":"9156_CR9","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.1038\/nm.4416","volume":"23","author":"LP Vu","year":"2017","unstructured":"Vu, L. P. et al. The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells. Nat. Med. 23, 1369\u20131376 (2017).","journal-title":"Nat. Med."},{"key":"9156_CR10","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/j.stem.2019.03.021","volume":"25","author":"J Paris","year":"2019","unstructured":"Paris, J. et al. Targeting the RNA m6A reader YTHDF2 selectively compromises cancer stem cells in acute myeloid leukemia. Cell Stem Cell 25, 137\u2013148.e6 (2019).","journal-title":"Cell Stem Cell"},{"key":"9156_CR11","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1038\/s41375-020-01066-4","volume":"35","author":"IA Elcheva","year":"2021","unstructured":"Elcheva, I. A. & Spiegelman, V. S. Targeting RNA-binding proteins in acute and chronic leukemia. Leukemia 35, 360\u2013376 (2021).","journal-title":"Leukemia"},{"key":"9156_CR12","doi-asserted-by":"publisher","first-page":"2493","DOI":"10.1182\/blood-2016-10-747436","volume":"129","author":"C Naudin","year":"2017","unstructured":"Naudin, C. et al. PUMILIO\/FOXP1 signaling drives expansion of hematopoietic stem\/progenitor and leukemia cells. Blood 129, 2493\u20132506 (2017).","journal-title":"Blood"},{"key":"9156_CR13","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1038\/nature10098","volume":"473","author":"B Schwanh\u00e4usser","year":"2011","unstructured":"Schwanh\u00e4usser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337\u2013342 (2011).","journal-title":"Nature"},{"key":"9156_CR14","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1016\/j.cell.2019.10.007","volume":"179","author":"DJ Clark","year":"2019","unstructured":"Clark, D. J. et al. Integrated proteogenomic characterization of clear cell renal cell carcinoma. Cell 179, 964\u2013983.e31 (2019).","journal-title":"Cell"},{"key":"9156_CR15","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1016\/j.cell.2019.03.030","volume":"177","author":"S Vasaikar","year":"2019","unstructured":"Vasaikar, S. et al. Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities. Cell 177, 1035\u20131049.e19 (2019).","journal-title":"Cell"},{"key":"9156_CR16","doi-asserted-by":"publisher","first-page":"1464","DOI":"10.1182\/bloodadvances.2020001652","volume":"4","author":"E-F Gautier","year":"2020","unstructured":"Gautier, E.-F. et al. Comprehensive proteomic analysis of murine terminal erythroid differentiation. Blood Adv. 4, 1464\u20131477 (2020).","journal-title":"Blood Adv."},{"key":"9156_CR17","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1038\/nature13319","volume":"509","author":"M Wilhelm","year":"2014","unstructured":"Wilhelm, M. et al. Mass-spectrometry-based draft of the human proteome. Nature 509, 582\u2013587 (2014).","journal-title":"Nature"},{"key":"9156_CR18","doi-asserted-by":"publisher","first-page":"e1005535","DOI":"10.1371\/journal.pcbi.1005535","volume":"13","author":"A Franks","year":"2017","unstructured":"Franks, A., Airoldi, E. & Slavov, N. Post-transcriptional regulation across human tissues. PLoS Comput. Biol. 13, e1005535 (2017).","journal-title":"PLoS Comput. Biol."},{"key":"9156_CR19","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20188513","volume":"15","author":"B Eraslan","year":"2019","unstructured":"Eraslan, B. et al. Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues. Mol. Syst. Biol. 15, e8513 (2019).","journal-title":"Mol. Syst. Biol."},{"key":"9156_CR20","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1038\/s41592-022-01526-y","volume":"19","author":"P Giansanti","year":"2022","unstructured":"Giansanti, P. et al. Mass spectrometry-based draft of the mouse proteome. Nat. Methods 19, 803\u2013811 (2022).","journal-title":"Nat. Methods"},{"key":"9156_CR21","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1038\/msb.2010.59","volume":"6","author":"C Vogel","year":"2010","unstructured":"Vogel, C. et al. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol. Syst. Biol. 6, 400 (2010).","journal-title":"Mol. Syst. Biol."},{"key":"9156_CR22","doi-asserted-by":"publisher","first-page":"1533","DOI":"10.1182\/blood.2022016033","volume":"140","author":"MH Kramer","year":"2022","unstructured":"Kramer, M. H. et al. Proteomic and phosphoproteomic landscapes of acute myeloid leukemia. Blood 140, 1533\u20131548 (2022).","journal-title":"Blood"},{"key":"9156_CR23","doi-asserted-by":"publisher","first-page":"3497","DOI":"10.1074\/mcp.M113.037309","volume":"13","author":"JR Wi\u015bniewski","year":"2014","unstructured":"Wi\u015bniewski, J. R., Hein, M. Y., Cox, J. & Mann, M. A. \u2018proteomic ruler\u2019 for protein copy number and concentration estimation without spike-in standards. Mol. Cell. Proteom. MCP 13, 3497\u20133506 (2014).","journal-title":"Mol. Cell. Proteom. MCP"},{"key":"9156_CR24","doi-asserted-by":"publisher","first-page":"706","DOI":"10.1038\/nature12946","volume":"505","author":"Y Wan","year":"2014","unstructured":"Wan, Y. et al. Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505, 706\u2013709 (2014).","journal-title":"Nature"},{"key":"9156_CR25","doi-asserted-by":"publisher","first-page":"1234","DOI":"10.1038\/s41592-022-01605-0","volume":"19","author":"HK Wayment-Steele","year":"2022","unstructured":"Wayment-Steele, H. K. et al. RNA secondary structure packages evaluated and improved by high-throughput experiments. Nat. Methods 19, 1234\u20131242 (2022).","journal-title":"Nat. Methods"},{"key":"9156_CR26","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1146\/annurev-biochem-060713-035802","volume":"83","author":"AG Hinnebusch","year":"2014","unstructured":"Hinnebusch, A. G. The scanning mechanism of eukaryotic translation initiation. Annu. Rev. Biochem. 83, 779\u2013812 (2014).","journal-title":"Annu. Rev. Biochem."},{"key":"9156_CR27","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1038\/nature13485","volume":"513","author":"AL Wolfe","year":"2014","unstructured":"Wolfe, A. L. et al. RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature 513, 65\u201370 (2014).","journal-title":"Nature"},{"key":"9156_CR28","doi-asserted-by":"publisher","first-page":"e1603","DOI":"10.1038\/cddis.2014.542","volume":"6","author":"A Modelska","year":"2015","unstructured":"Modelska, A. et al. The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape. Cell Death Dis. 6, e1603\u2013e1603 (2015).","journal-title":"Cell Death Dis."},{"key":"9156_CR29","doi-asserted-by":"publisher","first-page":"5336","DOI":"10.1093\/nar\/gkab287","volume":"49","author":"L Calviello","year":"2021","unstructured":"Calviello, L. et al. DDX3 depletion represses translation of mRNAs with complex 5\u2019 UTRs. Nucleic Acids Res 49, 5336\u20135350 (2021).","journal-title":"Nucleic Acids Res"},{"key":"9156_CR30","doi-asserted-by":"crossref","unstructured":"Jowhar, Z. et al. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. Mol. Syst. Biol. 20, 276\u2013290 (2024).","DOI":"10.1038\/s44320-024-00013-0"},{"key":"9156_CR31","doi-asserted-by":"publisher","DOI":"10.15252\/embj.2022112869","volume":"42","author":"Y Kito","year":"2023","unstructured":"Kito, Y. et al. The ASC-1 complex promotes translation initiation by scanning ribosomes. EMBO J. 42, e112869 (2023).","journal-title":"EMBO J."},{"key":"9156_CR32","doi-asserted-by":"publisher","first-page":"9521","DOI":"10.1093\/nar\/gkaa662","volume":"48","author":"J Steinberger","year":"2020","unstructured":"Steinberger, J. et al. Identification and characterization of hippuristanol-resistant mutants reveals eIF4A1 dependencies within mRNA 5\u2032 leader regions. Nucleic Acids Res. 48, 9521\u20139537 (2020).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR33","doi-asserted-by":"crossref","unstructured":"Lisi-Vega, L. E. et al. Bone marrow mesenchymal stromal cells support translation in refractory acute myeloid leukemia. Cell Rep. 44, 115151 (2025).","DOI":"10.1016\/j.celrep.2024.115151"},{"key":"9156_CR34","doi-asserted-by":"publisher","first-page":"D240","DOI":"10.1093\/nar\/gkac782","volume":"51","author":"S Bourdon","year":"2023","unstructured":"Bourdon, S. et al. QUADRatlas: the RNA G-quadruplex and RG4-binding proteins database. Nucleic Acids Res. 51, D240\u2013D247 (2023).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR35","doi-asserted-by":"publisher","first-page":"2629","DOI":"10.3389\/fmicb.2017.02629","volume":"8","author":"E Martinez-Salas","year":"2017","unstructured":"Martinez-Salas, E., Francisco-Velilla, R., Fernandez-Chamorro, J. & Embarek, A. M. Insights into structural and mechanistic features of viral IRES elements. Front. Microbiol. 8, 2629 (2017).","journal-title":"Front. Microbiol."},{"key":"9156_CR36","doi-asserted-by":"publisher","first-page":"4575","DOI":"10.1093\/nar\/gky282","volume":"46","author":"CS Lim","year":"2018","unstructured":"Lim, C. S., Wardell, T., Kleffmann, S. J. & Brown, T. C. M. The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. Nucleic Acids Res. 46, 4575\u20134591 (2018).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR37","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/nature10912","volume":"485","author":"AC Hsieh","year":"2012","unstructured":"Hsieh, A. C. et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature 485, 55\u201361 (2012).","journal-title":"Nature"},{"key":"9156_CR38","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1038\/nature11083","volume":"485","author":"CC Thoreen","year":"2012","unstructured":"Thoreen, C. C. et al. A unifying model for mTORC1-mediated regulation of mRNA translation. Nature 485, 109\u2013113 (2012).","journal-title":"Nature"},{"key":"9156_CR39","doi-asserted-by":"publisher","DOI":"10.1126\/science.aad4939","volume":"351","author":"S Weingarten-Gabbay","year":"2016","unstructured":"Weingarten-Gabbay, S. et al. Comparative genetics. Systematic discovery of cap-independent translation sequences in human and viral genomes. Science 351, aad4939 (2016).","journal-title":"Science"},{"key":"9156_CR40","doi-asserted-by":"publisher","first-page":"1413","DOI":"10.1126\/science.aad9868","volume":"352","author":"AG Hinnebusch","year":"2016","unstructured":"Hinnebusch, A. G., Ivanov, I. P. & Sonenberg, N. Translational control by 5\u2019-untranslated regions of eukaryotic mRNAs. Science 352, 1413\u20131416 (2016).","journal-title":"Science"},{"key":"9156_CR41","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1038\/s41587-019-0164-5","volume":"37","author":"PJ Sample","year":"2019","unstructured":"Sample, P. J. et al. Human 5\u2019 UTR design and variant effect prediction from a massively parallel translation assay. Nat. Biotechnol. 37, 803\u2013809 (2019).","journal-title":"Nat. Biotechnol."},{"key":"9156_CR42","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1126\/science.1168978","volume":"324","author":"NT Ingolia","year":"2009","unstructured":"Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218\u2013223 (2009).","journal-title":"Science"},{"key":"9156_CR43","doi-asserted-by":"publisher","first-page":"e1002866","DOI":"10.1371\/journal.pcbi.1002866","volume":"9","author":"L Ciandrini","year":"2013","unstructured":"Ciandrini, L., Stansfield, I. & Romano, M. C. Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation. PLoS Comput. Biol. 9, e1002866 (2013).","journal-title":"PLoS Comput. Biol."},{"key":"9156_CR44","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1016\/j.cell.2013.05.049","volume":"153","author":"P Shah","year":"2013","unstructured":"Shah, P., Ding, Y., Niemczyk, M., Kudla, G. & Plotkin, J. B. Rate-limiting steps in yeast protein translation. Cell 153, 1589\u20131601 (2013).","journal-title":"Cell"},{"key":"9156_CR45","doi-asserted-by":"publisher","first-page":"1787","DOI":"10.1016\/j.celrep.2016.01.043","volume":"14","author":"DE Weinberg","year":"2016","unstructured":"Weinberg, D. E. et al. Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation. Cell Rep. 14, 1787\u20131799 (2016).","journal-title":"Cell Rep."},{"key":"9156_CR46","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1007166","volume":"14","author":"KD Duc","year":"2018","unstructured":"Duc, K. D. & Song, Y. S. The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation. PLoS Genet. 14, e1007166 (2018).","journal-title":"PLoS Genet."},{"key":"9156_CR47","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1016\/j.cell.2018.02.036","volume":"173","author":"RK Khajuria","year":"2018","unstructured":"Khajuria, R. K. et al. Ribosome levels selectively regulate translation and lineage commitment in human hematopoiesis. Cell 173, 90\u2013103.e19 (2018).","journal-title":"Cell"},{"key":"9156_CR48","doi-asserted-by":"publisher","first-page":"746","DOI":"10.3324\/haematol.2019.239970","volume":"106","author":"I Boussaid","year":"2021","unstructured":"Boussaid, I. et al. Integrated analyses of translatome and proteome identify the rules of translation selectivity in RPS14-deficient cells. Haematologica 106, 746\u2013758 (2021).","journal-title":"Haematologica"},{"key":"9156_CR49","doi-asserted-by":"publisher","first-page":"2528","DOI":"10.1093\/nar\/gkw137","volume":"44","author":"C Sin","year":"2016","unstructured":"Sin, C., Chiarugi, D. & Valleriani, A. Quantitative assessment of ribosome drop-off in E. coli. Nucleic Acids Res. 44, 2528\u20132537 (2016).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR50","doi-asserted-by":"publisher","first-page":"e1005555","DOI":"10.1371\/journal.pcbi.1005555","volume":"13","author":"P Bonnin","year":"2017","unstructured":"Bonnin, P., Kern, N., Young, N. T., Stansfield, I. & Romano, M. C. Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile. PLoS Comput. Biol. 13, e1005555 (2017).","journal-title":"PLoS Comput. Biol."},{"key":"9156_CR51","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-17618-1","volume":"7","author":"LD Fernandes","year":"2017","unstructured":"Fernandes, L. D., Moura, A. P. S. de & Ciandrini, L. Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights. Sci. Rep. 7, 17409 (2017).","journal-title":"Sci. Rep."},{"key":"9156_CR52","doi-asserted-by":"crossref","unstructured":"Madern, M. F. et al. Long-term imaging of individual ribosomes reveals ribosome cooperativity in mRNA translation. Cell 188, 1896\u20131911.e24 (2025).","DOI":"10.1016\/j.cell.2025.01.016"},{"key":"9156_CR53","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.cell.2011.10.002","volume":"147","author":"NT Ingolia","year":"2011","unstructured":"Ingolia, N. T., Lareau, L. F. & Weissman, J. S. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789\u2013802 (2011).","journal-title":"Cell"},{"key":"9156_CR54","doi-asserted-by":"publisher","first-page":"985","DOI":"10.1093\/nar\/gkx1114","volume":"46","author":"AJ Diaz de Arce","year":"2018","unstructured":"Diaz de Arce, A. J., Noderer, W. L. & Wang, C. L. Complete motif analysis of sequence requirements for translation initiation at non-AUG start codons. Nucleic Acids Res. 46, 985\u2013994 (2018).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR55","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1009068","volume":"17","author":"T Kameda","year":"2021","unstructured":"Kameda, T., Asano, K. & Togashi, Y. Free energy landscape of RNA binding dynamics in start codon recognition by eukaryotic ribosomal pre-initiation complex. PLoS Comput. Biol. 17, e1009068 (2021).","journal-title":"PLoS Comput. Biol."},{"key":"9156_CR56","doi-asserted-by":"publisher","first-page":"8301","DOI":"10.1073\/pnas.87.21.8301","volume":"87","author":"M Kozak","year":"1990","unstructured":"Kozak, M. Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes. Proc. Natl. Acad. Sci. USA 87, 8301\u20138305 (1990).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"9156_CR57","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.molcel.2020.01.021","volume":"78","author":"JW Fischer","year":"2020","unstructured":"Fischer, J. W., Busa, V. F., Shao, Y. & Leung, A. K. L. Structure-mediated RNA decay by UPF1 and G3BP1. Mol. Cell 78, 70\u201384.e6 (2020).","journal-title":"Mol. Cell"},{"key":"9156_CR58","doi-asserted-by":"publisher","DOI":"10.15252\/embr.201948220","volume":"20","author":"F Hia","year":"2019","unstructured":"Hia, F. et al. Codon bias confers stability to human mRNAs. EMBO Rep. 20, e48220 (2019).","journal-title":"EMBO Rep."},{"key":"9156_CR59","doi-asserted-by":"publisher","DOI":"10.1186\/1745-6150-3-38","volume":"3","author":"P Puigb\u00f2","year":"2008","unstructured":"Puigb\u00f2, P., Bravo, I. G. & Garcia-Vallve, S. CAIcal: a combined set of tools to assess codon usage adaptation. Biol. Direct 3, 38 (2008).","journal-title":"Biol. Direct"},{"key":"9156_CR60","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1038\/nrg3965","volume":"16","author":"S Jonas","year":"2015","unstructured":"Jonas, S. & Izaurralde, E. Towards a molecular understanding of microRNA-mediated gene silencing. Nat. Rev. Genet. 16, 421\u2013433 (2015).","journal-title":"Nat. Rev. Genet."},{"key":"9156_CR61","doi-asserted-by":"crossref","unstructured":"Wu, Q. et al. Translation affects mRNA stability in a codon-dependent manner in human cells. eLife 8, e45396 (2019).","DOI":"10.7554\/eLife.45396"},{"key":"9156_CR62","doi-asserted-by":"crossref","unstructured":"Buschauer, R. et al. The Ccr4-Not complex monitors the translating ribosome for codon optimality. Science 368, eaay6912 (2020).","DOI":"10.1126\/science.aay6912"},{"key":"9156_CR63","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.1016\/j.cell.2015.02.029","volume":"160","author":"V Presnyak","year":"2015","unstructured":"Presnyak, V. et al. Codon optimality is a major determinant of mRNA stability. Cell 160, 1111\u20131124 (2015).","journal-title":"Cell"},{"key":"9156_CR64","doi-asserted-by":"publisher","first-page":"2087","DOI":"10.15252\/embj.201694699","volume":"35","author":"AA Bazzini","year":"2016","unstructured":"Bazzini, A. A. et al. Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. EMBO J. 35, 2087\u20132103 (2016).","journal-title":"EMBO J."},{"key":"9156_CR65","doi-asserted-by":"publisher","first-page":"9171","DOI":"10.1093\/nar\/gku646","volume":"42","author":"A Dana","year":"2014","unstructured":"Dana, A. & Tuller, T. The effect of tRNA levels on decoding times of mRNA codons. Nucleic Acids Res 42, 9171\u20139181 (2014).","journal-title":"Nucleic Acids Res"},{"key":"9156_CR66","doi-asserted-by":"publisher","first-page":"e0228730","DOI":"10.1371\/journal.pone.0228730","volume":"15","author":"ME Forrest","year":"2020","unstructured":"Forrest, M. E. et al. Codon and amino acid content are associated with mRNA stability in mammalian cells. PLoS ONE 15, e0228730 (2020).","journal-title":"PLoS ONE"},{"key":"9156_CR67","doi-asserted-by":"publisher","first-page":"1802","DOI":"10.1016\/j.molcel.2021.01.028","volume":"81","author":"A Behrens","year":"2021","unstructured":"Behrens, A., Rodschinka, G. & Nedialkova, D. D. High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq. Mol. Cell 81, 1802\u20131815.e7 (2021).","journal-title":"Mol. Cell"},{"key":"9156_CR68","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02811-x","volume":"23","author":"V Agarwal","year":"2022","unstructured":"Agarwal, V. & Kelley, D. R. The genetic and biochemical determinants of mRNA degradation rates in mammals. Genome Biol. 23, 245 (2022).","journal-title":"Genome Biol."},{"key":"9156_CR69","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005901","volume":"12","author":"X Lian","year":"2016","unstructured":"Lian, X. et al. Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells. PLoS Genet. 12, e1005901 (2016).","journal-title":"PLoS Genet."},{"key":"9156_CR70","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1016\/j.molcel.2017.09.003","volume":"68","author":"A Hubstenberger","year":"2017","unstructured":"Hubstenberger, A. et al. P-body purification reveals the condensation of repressed mRNA regulons. Mol. Cell 68, 144\u2013157.e5 (2017).","journal-title":"Mol. Cell"},{"key":"9156_CR71","doi-asserted-by":"publisher","first-page":"808","DOI":"10.1016\/j.molcel.2017.10.015","volume":"68","author":"A Khong","year":"2017","unstructured":"Khong, A. et al. The stress granule transcriptome reveals principles of mRNA accumulation in stress granules. Mol. Cell 68, 808\u2013820.e5 (2017).","journal-title":"Mol. Cell"},{"key":"9156_CR72","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1016\/j.cell.2019.05.027","volume":"178","author":"FM Fazal","year":"2019","unstructured":"Fazal, F. M. et al. Atlas of subcellular RNA localization revealed by APEX-Seq. Cell 178, 473\u2013490.e26 (2019).","journal-title":"Cell"},{"key":"9156_CR73","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1016\/j.molcel.2019.07.030","volume":"75","author":"A Padr\u00f3n","year":"2019","unstructured":"Padr\u00f3n, A., Iwasaki, S. & Ingolia, N. T. Proximity RNA labeling by APEX-Seq reveals the organization of translation initiation complexes and repressive RNA granules. Mol. Cell 75, 875\u2013887.e5 (2019).","journal-title":"Mol. Cell"},{"key":"9156_CR74","doi-asserted-by":"publisher","first-page":"D92","DOI":"10.1093\/nar\/gkt1248","volume":"42","author":"J-H Li","year":"2014","unstructured":"Li, J.-H., Liu, S., Zhou, H., Qu, L.-H. & Yang, J.-H. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 42, D92\u2013D97 (2014).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR75","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1038\/s41586-020-2077-3","volume":"583","author":"EL Van Nostrand","year":"2020","unstructured":"Van Nostrand, E. L. et al. A large-scale binding and functional map of human RNA-binding proteins. Nature 583, 711\u2013719 (2020).","journal-title":"Nature"},{"key":"9156_CR76","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baw035","volume":"2016","author":"G Giudice","year":"2016","unstructured":"Giudice, G., S\u00e1nchez-Cabo, F., Torroja, C. & Lara-Pezzi, E. ATtRACT\u2014a database of RNA-binding proteins and associated motifs. Database 2016, baw035 (2016).","journal-title":"Database"},{"key":"9156_CR77","doi-asserted-by":"publisher","first-page":"D327","DOI":"10.1093\/nar\/gkx934","volume":"46","author":"J-J Xuan","year":"2018","unstructured":"Xuan, J.-J. et al. RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data. Nucleic Acids Res. 46, D327\u2013D334 (2018).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR78","doi-asserted-by":"publisher","first-page":"D134","DOI":"10.1093\/nar\/gkaa692","volume":"49","author":"Y Tang","year":"2021","unstructured":"Tang, Y. et al. m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome. Nucleic Acids Res. 49, D134\u2013D143 (2021).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR79","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1038\/nmeth.4294","volume":"14","author":"Q Dai","year":"2017","unstructured":"Dai, Q. et al. Nm-seq maps 2\u2019-O-methylation sites in human mRNA with base precision. Nat. Methods 14, 695\u2013698 (2017).","journal-title":"Nat. Methods"},{"key":"9156_CR80","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1016\/j.molcel.2016.03.021","volume":"62","author":"S Lin","year":"2016","unstructured":"Lin, S., Choe, J., Du, P., Triboulet, R. & Gregory, R. I. The m(6)A methyltransferase METTL3 promotes translation in human cancer cells. Mol. Cell 62, 335\u2013345 (2016).","journal-title":"Mol. Cell"},{"key":"9156_CR81","doi-asserted-by":"publisher","first-page":"1872","DOI":"10.1016\/j.cell.2018.10.030","volume":"175","author":"D Arango","year":"2018","unstructured":"Arango, D. et al. Acetylation of cytidine in mrna promotes translation efficiency. Cell 175, 1872\u20131886.e24 (2018).","journal-title":"Cell"},{"key":"9156_CR82","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1038\/s41586-018-0538-8","volume":"561","author":"J Choe","year":"2018","unstructured":"Choe, J. et al. mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis. Nature 561, 556\u2013560 (2018).","journal-title":"Nature"},{"key":"9156_CR83","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1038\/s41586-021-03536-w","volume":"593","author":"E Yankova","year":"2021","unstructured":"Yankova, E. et al. Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia. Nature 593, 597\u2013601 (2021).","journal-title":"Nature"},{"key":"9156_CR84","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12518-6","volume":"10","author":"DA Kuppers","year":"2019","unstructured":"Kuppers, D. A. et al. N 6 -methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis. Nat. Commun. 10, 4596 (2019).","journal-title":"Nat. Commun."},{"key":"9156_CR85","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1016\/j.cell.2019.05.010","volume":"178","author":"S van Heesch","year":"2019","unstructured":"van Heesch, S. et al. The translational landscape of the human heart. Cell 178, 242\u2013260.e29 (2019).","journal-title":"Cell"},{"key":"9156_CR86","doi-asserted-by":"publisher","unstructured":"Wu, Q. et al. Translation of small downstream ORFs enhances translation of canonical main open reading frames. EMBO J. https:\/\/doi.org\/10.15252\/embj.2020104763 (2020).","DOI":"10.15252\/embj.2020104763"},{"key":"9156_CR87","doi-asserted-by":"publisher","first-page":"2885","DOI":"10.1016\/j.molcel.2022.06.023","volume":"82","author":"SP Chothani","year":"2022","unstructured":"Chothani, S. P. et al. A high-resolution map of human RNA translation. Mol. Cell 82, 2885\u20132899.e8 (2022).","journal-title":"Mol. Cell"},{"key":"9156_CR88","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1074\/mcp.RA118.000583","volume":"17","author":"J Zecha","year":"2018","unstructured":"Zecha, J. et al. Peptide level turnover measurements enable the study of proteoform dynamics. Mol. Cell. Proteom. MCP 17, 974\u2013992 (2018).","journal-title":"Mol. Cell. Proteom. MCP"},{"key":"9156_CR89","doi-asserted-by":"publisher","first-page":"1254","DOI":"10.1038\/s41592-019-0658-6","volume":"16","author":"W Ouyang","year":"2019","unstructured":"Ouyang, W. et al. Analysis of the human protein atlas image classification competition. Nat. Methods 16, 1254\u20131261 (2019).","journal-title":"Nat. Methods"},{"key":"9156_CR90","doi-asserted-by":"publisher","DOI":"10.1126\/scisignal.aaz0274","volume":"12","author":"M Uhl\u00e9n","year":"2019","unstructured":"Uhl\u00e9n, M. et al. The human secretome. Sci. Signal. 12, eaaz0274 (2019).","journal-title":"Sci. Signal."},{"key":"9156_CR91","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1016\/j.cell.2020.08.036","volume":"183","author":"L Jiang","year":"2020","unstructured":"Jiang, L. et al. A quantitative proteome map of the human body. Cell 183, 269\u2013283.e19 (2020).","journal-title":"Cell"},{"key":"9156_CR92","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1038\/nature13302","volume":"509","author":"M-S Kim","year":"2014","unstructured":"Kim, M.-S. et al. A draft map of the human proteome. Nature 509, 575\u2013581 (2014).","journal-title":"Nature"},{"key":"9156_CR93","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20188503","volume":"15","author":"D Wang","year":"2019","unstructured":"Wang, D. et al. A deep proteome and transcriptome abundance atlas of 29 healthy human tissues. Mol. Syst. Biol. 15, e8503 (2019).","journal-title":"Mol. Syst. Biol."},{"key":"9156_CR94","doi-asserted-by":"publisher","first-page":"2594","DOI":"10.1182\/blood.2021014241","volume":"140","author":"M Janssen","year":"2022","unstructured":"Janssen, M. et al. Venetoclax synergizes with gilteritinib in FLT3 wild-type high-risk acute myeloid leukemia by suppressing MCL-1. Blood 140, 2594\u20132610 (2022).","journal-title":"Blood"},{"key":"9156_CR95","doi-asserted-by":"publisher","first-page":"1720","DOI":"10.1158\/2159-8290.CD-22-0411","volume":"13","author":"M Sabatier","year":"2023","unstructured":"Sabatier, M. et al. C\/EBP\u03b1 confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress\u2013induced ferroptosis in FLT3-mutant leukemia. Cancer Discov. 13, 1720\u20131747 (2023).","journal-title":"Cancer Discov."},{"key":"9156_CR96","doi-asserted-by":"publisher","first-page":"4191","DOI":"10.1016\/j.molcel.2024.09.011","volume":"84","author":"A Safieddine","year":"2024","unstructured":"Safieddine, A. et al. Cell-cycle-dependent mRNA localization in P-bodies. Mol. Cell 84, 4191\u20134208.e7 (2024).","journal-title":"Mol. Cell"},{"key":"9156_CR97","doi-asserted-by":"publisher","first-page":"1789","DOI":"10.1021\/acschembio.2c00145","volume":"17","author":"JC Swartzel","year":"2022","unstructured":"Swartzel, J. C. et al. Targeted degradation of mRNA decapping enzyme DcpS by a VHL-recruiting PROTAC. ACS Chem. Biol. 17, 1789\u20131798 (2022).","journal-title":"ACS Chem. Biol."},{"key":"9156_CR98","doi-asserted-by":"publisher","DOI":"10.1038\/srep16688","volume":"5","author":"O Meziane","year":"2015","unstructured":"Meziane, O. et al. The human decapping scavenger enzyme DcpS modulates microRNA turnover. Sci. Rep. 5, 16688 (2015).","journal-title":"Sci. Rep."},{"key":"9156_CR99","doi-asserted-by":"publisher","first-page":"2484","DOI":"10.1038\/s41375-020-0768-2","volume":"34","author":"S Zhu","year":"2020","unstructured":"Zhu, S. et al. Restoration of microRNA function impairs MYC-dependent maintenance of MLL leukemia. Leukemia 34, 2484\u20132488 (2020).","journal-title":"Leukemia"},{"key":"9156_CR100","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1038\/nrm.2017.103","volume":"19","author":"K Leppek","year":"2018","unstructured":"Leppek, K., Das, R. & Barna, M. Functional 5\u2019 UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat. Rev. Mol. Cell Biol. 19, 158\u2013174 (2018).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"9156_CR101","doi-asserted-by":"publisher","unstructured":"Jia, L. et al. Decoding mRNA translatability and stability from the 5\u2032UTR. Nat. Struct. Mol. Biol. 1\u20138 https:\/\/doi.org\/10.1038\/s41594-020-0465-x (2020).","DOI":"10.1038\/s41594-020-0465-x"},{"key":"9156_CR102","doi-asserted-by":"publisher","first-page":"706","DOI":"10.15252\/embj.201592759","volume":"35","author":"TG Johnstone","year":"2016","unstructured":"Johnstone, T. G., Bazzini, A. A. & Giraldez, A. J. Upstream ORFs are prevalent translational repressors in vertebrates. EMBO J. 35, 706\u2013723 (2016).","journal-title":"EMBO J."},{"key":"9156_CR103","doi-asserted-by":"publisher","unstructured":"Zheng, D. et al. Predicting the translation efficiency of messenger RNA in mammalian cells. Nat. Biotechnol. 1\u201314 https:\/\/doi.org\/10.1038\/s41587-025-02712-x (2025).","DOI":"10.1038\/s41587-025-02712-x"},{"key":"9156_CR104","doi-asserted-by":"crossref","unstructured":"Murakami, S. et al. m6A alters ribosome dynamics to initiate mRNA degradation. Cell 0, 3728\u20133743 (2025).","DOI":"10.1016\/j.cell.2025.04.020"},{"key":"9156_CR105","doi-asserted-by":"crossref","unstructured":"Linder, B. et al. tRNA modifications tune m6A-dependent mRNA decay. Cell 0, 13 (2025).","DOI":"10.1016\/j.cell.2025.04.013"},{"key":"9156_CR106","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/j.molcel.2022.12.026","volume":"83","author":"A Uzonyi","year":"2023","unstructured":"Uzonyi, A. et al. Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability. Mol. Cell 83, 237\u2013251.e7 (2023).","journal-title":"Mol. Cell"},{"key":"9156_CR107","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35643-1","volume":"13","author":"X Yang","year":"2022","unstructured":"Yang, X., Triboulet, R., Liu, Q., Sendinc, E. & Gregory, R. I. Exon junction complex shapes the m6A epitranscriptome. Nat. Commun. 13, 7904 (2022).","journal-title":"Nat. Commun."},{"key":"9156_CR108","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adp5689","volume":"10","author":"Q Li","year":"2024","unstructured":"Li, Q. et al. Decoding the interplay between m6A modification and stress granule stability by live-cell imaging. Sci. Adv. 10, eadp5689 (2024).","journal-title":"Sci. Adv."},{"key":"9156_CR109","doi-asserted-by":"publisher","first-page":"4576","DOI":"10.1016\/j.molcel.2024.10.033","volume":"84","author":"Y Zhou","year":"2024","unstructured":"Zhou, Y. et al. m6A sites in the coding region trigger translation-dependent mRNA decay. Mol. Cell 84, 4576\u20134593.e12 (2024).","journal-title":"Mol. Cell"},{"key":"9156_CR110","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-020-00769-5","volume":"18","author":"U Schumann","year":"2020","unstructured":"Schumann, U. et al. Multiple links between 5-methylcytosine content of mRNA and translation. BMC Biol. 18, 40 (2020).","journal-title":"BMC Biol."},{"key":"9156_CR111","doi-asserted-by":"publisher","first-page":"2320","DOI":"10.1016\/j.molcel.2024.04.011","volume":"84","author":"Y Li","year":"2024","unstructured":"Li, Y. et al. 2\u2019-O-methylation at internal sites on mRNA promotes mRNA stability. Mol. Cell 84, 2320\u20132336.e6 (2024).","journal-title":"Mol. Cell"},{"key":"9156_CR112","doi-asserted-by":"publisher","first-page":"1610","DOI":"10.1101\/gr.193342.115","volume":"25","author":"C Cenik","year":"2015","unstructured":"Cenik, C. et al. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. Genome Res. 25, 1610\u20131621 (2015).","journal-title":"Genome Res."},{"key":"9156_CR113","doi-asserted-by":"publisher","first-page":"1717","DOI":"10.1101\/gad.305250.117","volume":"31","author":"MG Kearse","year":"2017","unstructured":"Kearse, M. G. & Wilusz, J. E. Non-AUG translation: a new start for protein synthesis in eukaryotes. Genes Dev. 31, 1717\u20131731 (2017).","journal-title":"Genes Dev."},{"key":"9156_CR114","doi-asserted-by":"publisher","first-page":"3608","DOI":"10.1002\/j.1460-2075.1994.tb06668.x","volume":"13","author":"R Boeck","year":"1994","unstructured":"Boeck, R. & Kolakofsky, D. Positions +5 and +6 can be major determinants of the efficiency of non-AUG initiation codons for protein synthesis. EMBO J. 13, 3608\u20133617 (1994).","journal-title":"EMBO J."},{"key":"9156_CR115","doi-asserted-by":"publisher","first-page":"3618","DOI":"10.1002\/j.1460-2075.1994.tb06669.x","volume":"13","author":"S Gr\u00fcnert","year":"1994","unstructured":"Gr\u00fcnert, S. & Jackson, R. J. The immediate downstream codon strongly influences the efficiency of utilization of eukaryotic translation initiation codons. EMBO J. 13, 3618\u20133630 (1994).","journal-title":"EMBO J."},{"key":"9156_CR116","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1038\/nature13007","volume":"508","author":"AO Subtelny","year":"2014","unstructured":"Subtelny, A. O., Eichhorn, S. W., Chen, G. R., Sive, H. & Bartel, D. P. Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508, 66\u201371 (2014).","journal-title":"Nature"},{"key":"9156_CR117","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.66493","volume":"10","author":"K Xiang","year":"2021","unstructured":"Xiang, K. & Bartel, D. P. The molecular basis of coupling between poly(A)-tail length and translational efficiency. eLife 10, e66493 (2021).","journal-title":"eLife"},{"key":"9156_CR118","doi-asserted-by":"publisher","first-page":"e1002603","DOI":"10.1371\/journal.pgen.1002603","volume":"8","author":"W Qian","year":"2012","unstructured":"Qian, W., Yang, J.-R., Pearson, N. M., Maclean, C. & Zhang, J. Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet. 8, e1002603 (2012).","journal-title":"PLoS Genet."},{"key":"9156_CR119","doi-asserted-by":"publisher","first-page":"15023","DOI":"10.1073\/pnas.1817299116","volume":"116","author":"A Riba","year":"2019","unstructured":"Riba, A. et al. Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates. Proc. Natl. Acad. Sci. USA 116, 15023\u201315032 (2019).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"9156_CR120","doi-asserted-by":"publisher","first-page":"4474","DOI":"10.1016\/j.cell.2022.10.005","volume":"185","author":"J Wang","year":"2022","unstructured":"Wang, J. et al. Rapid 40S scanning and its regulation by mRNA structure during eukaryotic translation initiation. Cell 185, 4474\u20134487.e17 (2022).","journal-title":"Cell"},{"key":"9156_CR121","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.molcel.2007.03.002","volume":"26","author":"DH Lackner","year":"2007","unstructured":"Lackner, D. H. et al. A network of multiple regulatory layers shapes gene expression in fission yeast. Mol. Cell 26, 145\u2013155 (2007).","journal-title":"Mol. Cell"},{"key":"9156_CR122","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1039\/C4MB00462K","volume":"11","author":"J Guo","year":"2015","unstructured":"Guo, J., Lian, X., Zhong, J., Wang, T. & Zhang, G. Length-dependent translation initiation benefits the functional proteome of human cells. Mol. BioSyst. 11, 370\u2013378 (2015).","journal-title":"Mol. BioSyst."},{"key":"9156_CR123","doi-asserted-by":"crossref","unstructured":"Jeacock, L., Faria, J. & Horn, D. Codon usage bias controls mRNA and protein abundance in trypanosomatids. eLife 7, e32496 (2018).","DOI":"10.7554\/eLife.32496"},{"key":"9156_CR124","doi-asserted-by":"publisher","first-page":"1276","DOI":"10.1038\/nature06974","volume":"453","author":"N Amrani","year":"2008","unstructured":"Amrani, N., Ghosh, S., Mangus, D. A. & Jacobson, A. Translation factors promote the formation of two states of the closed-loop mRNP. Nature 453, 1276\u20131280 (2008).","journal-title":"Nature"},{"key":"9156_CR125","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0559-z","volume":"16","author":"J Costello","year":"2015","unstructured":"Costello, J. et al. Global mRNA selection mechanisms for translation initiation. Genome Biol. 16, 10 (2015).","journal-title":"Genome Biol."},{"key":"9156_CR126","doi-asserted-by":"publisher","unstructured":"Thompson, M. K. & Gilbert, W. V. mRNA length-sensing in eukaryotic translation: reconsidering the \u2018closed loop\u2019 and its implications for translational control. Curr. Genet. https:\/\/doi.org\/10.1007\/s00294-016-0674-3 (2016).","DOI":"10.1007\/s00294-016-0674-3"},{"key":"9156_CR127","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1016\/j.molcel.2018.10.047","volume":"72","author":"Q Vicens","year":"2018","unstructured":"Vicens, Q., Kieft, J. S. & Rissland, O. S. Revisiting the closed-loop model and the nature of mRNA 5\u2032\u20133\u2032 communication. Mol. Cell 72, 805\u2013812 (2018).","journal-title":"Mol. Cell"},{"key":"9156_CR128","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1007\/978-3-030-31434-7_6","volume":"1203","author":"H Fakim","year":"2019","unstructured":"Fakim, H. & Fabian, M. R. Communication is key: 5\u2019-3\u2019 interactions that regulate mRNA translation and turnover. Adv. Exp. Med. Biol. 1203, 149\u2013164 (2019).","journal-title":"Adv. Exp. Med. Biol."},{"key":"9156_CR129","doi-asserted-by":"publisher","first-page":"8240","DOI":"10.1093\/nar\/gkac631","volume":"50","author":"B \u00c7etin","year":"2022","unstructured":"\u00c7etin, B. & O\u2019Leary, S. E. mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation. Nucleic Acids Res 50, 8240\u20138261 (2022).","journal-title":"Nucleic Acids Res"},{"key":"9156_CR130","doi-asserted-by":"crossref","unstructured":"Rogers, D. W., B\u00f6ttcher, M. A., Traulsen, A. & Greig, D. Ribosome reinitiation can explain length-dependent translation of messenger RNA. PLoS Comput. Biol. 13, e1005592 (2017).","DOI":"10.1371\/journal.pcbi.1005592"},{"key":"9156_CR131","doi-asserted-by":"crossref","unstructured":"Alekhina, O. M., Terenin, I. M., Dmitriev, S. E. & Vassilenko, K. S. Functional cyclization of eukaryotic mRNAs. Int. J. Mol. Sci. 21, 1677 (2020).","DOI":"10.3390\/ijms21051677"},{"key":"9156_CR132","doi-asserted-by":"publisher","first-page":"113413","DOI":"10.1016\/j.celrep.2023.113413","volume":"42","author":"CL Barrington","year":"2023","unstructured":"Barrington, C. L. et al. Synonymous codon usage regulates translation initiation. Cell Rep. 42, 113413 (2023).","journal-title":"Cell Rep."},{"key":"9156_CR133","doi-asserted-by":"publisher","unstructured":"Lyons, E. F. et al. Codon optimality modulates protein output by tuning translation initiation. bioRxiv 2023.11.27.568910 https:\/\/doi.org\/10.1101\/2023.11.27.568910 (2023).","DOI":"10.1101\/2023.11.27.568910"},{"key":"9156_CR134","doi-asserted-by":"publisher","first-page":"114098","DOI":"10.1016\/j.celrep.2024.114098","volume":"43","author":"AA Bicknell","year":"2024","unstructured":"Bicknell, A. A. et al. Attenuating ribosome load improves protein output from mRNA by limiting translation-dependent mRNA decay. Cell Rep. 43, 114098 (2024).","journal-title":"Cell Rep."},{"key":"9156_CR135","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1128\/MCB.16.1.146","volume":"16","author":"RL Tanguay","year":"1996","unstructured":"Tanguay, R. L. & Gallie, D. R. Translational efficiency is regulated by the length of the 3\u2019 untranslated region. Mol. Cell. Biol. 16, 146\u2013156 (1996).","journal-title":"Mol. Cell. Biol."},{"key":"9156_CR136","doi-asserted-by":"publisher","first-page":"1900","DOI":"10.1074\/mcp.M112.025783","volume":"12","author":"Q Liu","year":"2013","unstructured":"Liu, Q. et al. Integrative omics analysis reveals the importance and scope of translational repression in microRNA-mediated regulation*. Mol. Cell. Proteom. 12, 1900\u20131911 (2013).","journal-title":"Mol. Cell. Proteom."},{"key":"9156_CR137","doi-asserted-by":"publisher","first-page":"e00313","DOI":"10.1128\/MCB.00313-19","volume":"39","author":"T Matheny","year":"2019","unstructured":"Matheny, T., Rao, B. S. & Parker, R. Transcriptome-wide comparison of stress granules and P-bodies reveals that translation plays a major role in RNA partitioning. Mol. Cell. Biol. 39, e00313\u2013e00319 (2019).","journal-title":"Mol. Cell. Biol."},{"key":"9156_CR138","doi-asserted-by":"publisher","first-page":"112211","DOI":"10.1016\/j.celrep.2023.112211","volume":"42","author":"N Curdy","year":"2023","unstructured":"Curdy, N. et al. The proteome and transcriptome of stress granules and P bodies during human T lymphocyte activation. Cell Rep. 42, 112211 (2023).","journal-title":"Cell Rep."},{"key":"9156_CR139","doi-asserted-by":"publisher","first-page":"3966","DOI":"10.1016\/j.febslet.2009.10.036","volume":"583","author":"T Maier","year":"2009","unstructured":"Maier, T., G\u00fcell, M. & Serrano, L. Correlation of mRNA and protein in complex biological samples. FEBS Lett. 583, 3966\u20133973 (2009).","journal-title":"FEBS Lett."},{"key":"9156_CR140","doi-asserted-by":"publisher","first-page":"D988","DOI":"10.1093\/nar\/gkab1049","volume":"50","author":"F Cunningham","year":"2022","unstructured":"Cunningham, F. et al. Ensembl 2022. Nucleic Acids Res 50, D988\u2013D995 (2022).","journal-title":"Nucleic Acids Res"},{"key":"9156_CR141","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/1748-7188-6-26","volume":"6","author":"R Lorenz","year":"2011","unstructured":"Lorenz, R. et al. ViennaRNA Package 2.0. Algorithms Mol. Biol. 6, 26 (2011).","journal-title":"Algorithms Mol. Biol."},{"key":"9156_CR142","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1016\/j.gpb.2020.03.001","volume":"18","author":"J Zhao","year":"2020","unstructured":"Zhao, J. et al. IRESbase: a comprehensive database of experimentally validated internal ribosome entry sites. Genomics Proteom. Bioinforma. 18, 129\u2013139 (2020).","journal-title":"Genomics Proteom. Bioinforma."},{"key":"9156_CR143","doi-asserted-by":"publisher","first-page":"D131","DOI":"10.1093\/nar\/gkp981","volume":"38","author":"M Mokrejs","year":"2010","unstructured":"Mokrejs, M. et al. IRESite-a tool for the examination of viral and cellular internal ribosome entry sites. Nucleic Acids Res. 38, D131\u2013D136 (2010).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR144","doi-asserted-by":"publisher","first-page":"902","DOI":"10.1126\/science.1123835","volume":"312","author":"A Yoon","year":"2006","unstructured":"Yoon, A. et al. Impaired control of IRES-mediated translation in X-linked dyskeratosis congenita. Science 312, 902\u2013906 (2006).","journal-title":"Science"},{"key":"9156_CR145","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1038\/nmeth.3688","volume":"13","author":"L Calviello","year":"2016","unstructured":"Calviello, L. et al. Detecting actively translated open reading frames in ribosome profiling data. Nat. Methods 13, 165\u2013170 (2016).","journal-title":"Nat. Methods"},{"key":"9156_CR146","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-01981-8","volume":"8","author":"P Zhang","year":"2017","unstructured":"Zhang, P. et al. Genome-wide identification and differential analysis of translational initiation. Nat. Commun. 8, 1749 (2017).","journal-title":"Nat. Commun."},{"key":"9156_CR147","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1038\/nmeth.4631","volume":"15","author":"F Erhard","year":"2018","unstructured":"Erhard, F. et al. Improved Ribo-seq enables identification of cryptic translation events. Nat. Methods 15, 363\u2013366 (2018).","journal-title":"Nat. Methods"},{"key":"9156_CR148","doi-asserted-by":"publisher","first-page":"W361","DOI":"10.1093\/nar\/gku406","volume":"42","author":"I Paz","year":"2014","unstructured":"Paz, I., Kosti, I., Manuel Ares, J., Cline, M. & Mandel-Gutfreund, Y. RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res. 42, W361 (2014).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR149","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1038\/nature12311","volume":"499","author":"D Ray","year":"2013","unstructured":"Ray, D. et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature 499, 172\u2013177 (2013).","journal-title":"Nature"},{"key":"9156_CR150","doi-asserted-by":"publisher","first-page":"D127","DOI":"10.1093\/nar\/gkz757","volume":"48","author":"Y Chen","year":"2020","unstructured":"Chen, Y. & Wang, X. miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res. 48, D127\u2013D131 (2020).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR151","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1629-z","volume":"20","author":"W Liu","year":"2019","unstructured":"Liu, W. & Wang, X. Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data. Genome Biol. 20, 18 (2019).","journal-title":"Genome Biol."},{"key":"9156_CR152","doi-asserted-by":"publisher","DOI":"10.1126\/science.aav1741","volume":"366","author":"SE McGeary","year":"2019","unstructured":"McGeary, S. E. et al. The biochemical basis of microRNA targeting efficacy. Science 366, eaav1741 (2019).","journal-title":"Science"},{"key":"9156_CR153","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.05005","volume":"4","author":"V Agarwal","year":"2015","unstructured":"Agarwal, V., Bell, G. W., Nam, J.-W. & Bartel, D. P. Predicting effective microRNA target sites in mammalian mRNAs. eLife 4, e05005 (2015).","journal-title":"eLife"},{"key":"9156_CR154","doi-asserted-by":"publisher","first-page":"879","DOI":"10.1038\/s41592-019-0503-y","volume":"16","author":"I Legnini","year":"2019","unstructured":"Legnini, I., Alles, J., Karaiskos, N., Ayoub, S. & Rajewsky, N. FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control. Nat. Methods 16, 879\u2013886 (2019).","journal-title":"Nat. Methods"},{"key":"9156_CR155","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1038\/s41592-019-0617-2","volume":"16","author":"RE Workman","year":"2019","unstructured":"Workman, R. E. et al. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nat. Methods 16, 1297\u20131305 (2019).","journal-title":"Nat. Methods"},{"key":"9156_CR156","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/s41592-022-01714-w","volume":"20","author":"O Begik","year":"2023","unstructured":"Begik, O. et al. Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing. Nat. Methods 20, 75\u201385 (2023).","journal-title":"Nat. Methods"},{"key":"9156_CR157","doi-asserted-by":"publisher","first-page":"1332","DOI":"10.1101\/gr.257857.119","volume":"30","author":"KC Maier","year":"2020","unstructured":"Maier, K. C., Gressel, S., Cramer, P. & Schwalb, B. Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms. Genome Res. 30, 1332 (2020).","journal-title":"Genome Res."},{"key":"9156_CR158","doi-asserted-by":"publisher","first-page":"1044","DOI":"10.1016\/j.molcel.2014.02.007","volume":"53","author":"H Chang","year":"2014","unstructured":"Chang, H., Lim, J., Ha, M. & Kim, V. N. TAIL-seq: genome-wide determination of poly(A) tail length and 3\u2019 end modifications. Mol. Cell 53, 1044\u20131052 (2014).","journal-title":"Mol. Cell"},{"key":"9156_CR159","doi-asserted-by":"publisher","first-page":"e0234696","DOI":"10.1371\/journal.pone.0234696","volume":"15","author":"F Yu","year":"2020","unstructured":"Yu, F. et al. Poly(A)-seq: a method for direct sequencing and analysis of the transcriptomic poly(A)-tails. PLoS ONE 15, e0234696 (2020).","journal-title":"PLoS ONE"},{"key":"9156_CR160","doi-asserted-by":"publisher","first-page":"5125","DOI":"10.1093\/nar\/14.13.5125","volume":"14","author":"PM Sharp","year":"1986","unstructured":"Sharp, P. M., Tuohy, T. M. & Mosurski, K. R. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14, 5125\u20135143 (1986).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR161","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1093\/nar\/15.3.1281","volume":"15","author":"PM Sharp","year":"1987","unstructured":"Sharp, P. M. & Li, W. H. The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281\u20131295 (1987).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR162","doi-asserted-by":"publisher","first-page":"5036","DOI":"10.1093\/nar\/gkh834","volume":"32","author":"M dos Reis","year":"2004","unstructured":"dos Reis, M., Savva, R. & Wernisch, L. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res. 32, 5036\u20135044 (2004).","journal-title":"Nucleic Acids Res."},{"key":"9156_CR163","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1038\/nmeth.3478","volume":"12","author":"G Zheng","year":"2015","unstructured":"Zheng, G. et al. Efficient and quantitative high-throughput tRNA sequencing. Nat. Methods 12, 835\u2013837 (2015).","journal-title":"Nat. Methods"},{"key":"9156_CR164","doi-asserted-by":"publisher","unstructured":"Narula, A., Ellis, J., Taliaferro, J. M. & Rissland, O. S. Coding regions affect mRNA stability in human cells. RNA 073239.119 https:\/\/doi.org\/10.1261\/rna.073239.119 (2019).","DOI":"10.1261\/rna.073239.119"},{"key":"9156_CR165","doi-asserted-by":"publisher","first-page":"4494","DOI":"10.1016\/j.molcel.2023.10.040","volume":"83","author":"T Shan","year":"2023","unstructured":"Shan, T. et al. m6A modification negatively regulates translation by switching mRNA from polysome to P-body via IGF2BP3. Mol. Cell 83, 4494\u20134508.e6 (2023).","journal-title":"Mol. Cell"},{"key":"9156_CR166","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-43194-2","volume":"14","author":"Z Ren","year":"2023","unstructured":"Ren, Z., Tang, W., Peng, L. & Zou, P. Profiling stress-triggered RNA condensation with photocatalytic proximity labeling. Nat. Commun. 14, 7390 (2023).","journal-title":"Nat. Commun."},{"key":"9156_CR167","doi-asserted-by":"publisher","first-page":"3551","DOI":"10.1074\/mcp.M116.063230","volume":"15","author":"KA Welle","year":"2016","unstructured":"Welle, K. A. et al. Time-resolved analysis of proteome dynamics by tandem mass tags and stable isotope labeling in cell culture (TMT-SILAC) hyperplexing. Mol. Cell. Proteom. MCP 15, 3551\u20133563 (2016).","journal-title":"Mol. Cell. Proteom. MCP"},{"key":"9156_CR168","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1021\/pr800641v","volume":"8","author":"MK Doherty","year":"2009","unstructured":"Doherty, M. K., Hammond, D. E., Clague, M. J., Gaskell, S. J. & Beynon, R. J. Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC. J. Proteome Res. 8, 104\u2013112 (2009).","journal-title":"J. Proteome Res."},{"key":"9156_CR169","doi-asserted-by":"publisher","first-page":"5275","DOI":"10.1021\/pr101183k","volume":"10","author":"SB Cambridge","year":"2011","unstructured":"Cambridge, S. B. et al. Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover. J. Proteome Res. 10, 5275\u20135284 (2011).","journal-title":"J. Proteome Res."},{"key":"9156_CR170","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M111.011429","volume":"11","author":"F-M Boisvert","year":"2012","unstructured":"Boisvert, F.-M. et al. A quantitative spatial proteomics analysis of proteome turnover in human cells*. Mol. Cell. Proteom. 11, M111.011429 (2012).","journal-title":"Mol. Cell. Proteom."},{"key":"9156_CR171","doi-asserted-by":"publisher","unstructured":"Korotkevich, G. et al. Fast gene set enrichment analysis. 060012 Preprint at https:\/\/doi.org\/10.1101\/060012 (2021).","DOI":"10.1101\/060012"},{"key":"9156_CR172","doi-asserted-by":"publisher","unstructured":"Smilkov, D. et al. Embedding projector: interactive visualization and interpretation of embeddings. Preprint at https:\/\/doi.org\/10.48550\/arXiv.1611.05469 (2016).","DOI":"10.48550\/arXiv.1611.05469"},{"key":"9156_CR173","doi-asserted-by":"publisher","first-page":"1835","DOI":"10.1021\/acs.jmedchem.0c01489","volume":"64","author":"JD Hansen","year":"2021","unstructured":"Hansen, J. D. et al. CC-90009: a cereblon E3 ligase modulating drug that promotes selective degradation of GSPT1 for the treatment of acute myeloid leukemia. J. Med. Chem. 64, 1835\u20131843 (2021).","journal-title":"J. Med. Chem."},{"key":"9156_CR174","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.adk1731","volume":"16","author":"C Larrue","year":"2024","unstructured":"Larrue, C. et al. Targeting ferritinophagy impairs quiescent cancer stem cells in acute myeloid leukemia in vitro and in vivo models. Sci. Transl. Med. 16, eadk1731 (2024).","journal-title":"Sci. Transl. Med."},{"key":"9156_CR175","doi-asserted-by":"crossref","unstructured":"Sellar, R. S. et al. Degradation of GSPT1 causes TP53-independent cell death in leukemia while sparing normal hematopoietic stem cells. J. Clin. Investig. 132, e153514 (2022).","DOI":"10.1172\/JCI153514"},{"key":"9156_CR176","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1016\/j.ccell.2023.02.010","volume":"41","author":"S-M Park","year":"2023","unstructured":"Park, S.-M. et al. Dual IKZF2 and CK1\u03b1 degrader targets acute myeloid leukemia cells. Cancer Cell 41, 726\u2013739.e11 (2023).","journal-title":"Cancer Cell"},{"key":"9156_CR177","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abn3248","volume":"14","author":"W Grey","year":"2022","unstructured":"Grey, W. et al. CKS1 inhibition depletes leukemic stem cells and protects healthy hematopoietic stem cells in acute myeloid leukemia. Sci. Transl. Med. 14, eabn3248 (2022).","journal-title":"Sci. Transl. Med."},{"key":"9156_CR178","doi-asserted-by":"publisher","first-page":"674","DOI":"10.1016\/j.ccell.2018.08.014","volume":"34","author":"B de Boer","year":"2018","unstructured":"de Boer, B. et al. Prospective isolation and characterization of genetically and functionally distinct AML subclones. Cancer Cell 34, 674\u2013689.e8 (2018).","journal-title":"Cancer Cell"},{"key":"9156_CR179","doi-asserted-by":"publisher","first-page":"24734","DOI":"10.18632\/aging.202361","volume":"12","author":"M Hernandez-Valladares","year":"2020","unstructured":"Hernandez-Valladares, M., Aaseb\u00f8, E., Berven, F., Selheim, F. & Bruserud, \u00d8 Biological characteristics of aging in human acute myeloid leukemia cells: the possible importance of aldehyde dehydrogenase, the cytoskeleton and altered transcriptional regulation. Aging 12, 24734\u201324777 (2020).","journal-title":"Aging"},{"key":"9156_CR180","doi-asserted-by":"publisher","first-page":"11","DOI":"10.3390\/proteomes6010011","volume":"6","author":"JR Schmidt","year":"2018","unstructured":"Schmidt, J. R. et al. Pilot study on mass spectrometry-based analysis of the proteome of CD34+CD123+ progenitor cells for the identification of potential targets for immunotherapy in acute myeloid leukemia. Proteomes 6, 11 (2018).","journal-title":"Proteomes"},{"key":"9156_CR181","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1158\/2159-8290.CD-22-0210","volume":"13","author":"F Zhou","year":"2023","unstructured":"Zhou, F. et al. A dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia. Cancer Discov. 13, 332\u2013347 (2023).","journal-title":"Cancer Discov."},{"key":"9156_CR182","doi-asserted-by":"publisher","first-page":"2059","DOI":"10.1182\/blood.2019004121","volume":"135","author":"C Pauli","year":"2020","unstructured":"Pauli, C. et al. Site-specific methylation of 18S ribosomal RNA by SNORD42A is required for acute myeloid leukemia cell proliferation. Blood 135, 2059\u20132070 (2020).","journal-title":"Blood"},{"key":"9156_CR183","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1038\/s41392-022-01288-1","volume":"8","author":"P Casado","year":"2023","unstructured":"Casado, P. et al. Integrative phosphoproteomics defines two biologically distinct groups of KMT2A rearranged acute myeloid leukaemia with different drug response phenotypes. Signal Transduct. Target. Ther. 8, 80 (2023).","journal-title":"Signal Transduct. Target. Ther."},{"key":"9156_CR184","doi-asserted-by":"publisher","first-page":"111177","DOI":"10.1016\/j.celrep.2022.111177","volume":"40","author":"KB Emdal","year":"2022","unstructured":"Emdal, K. B. et al. Phosphoproteomics of primary AML patient samples reveals rationale for AKT combination therapy and p53 context to overcome selinexor resistance. Cell Rep. 40, 111177 (2022).","journal-title":"Cell Rep."},{"key":"9156_CR185","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1016\/j.ccell.2022.02.006","volume":"40","author":"AK Jayavelu","year":"2022","unstructured":"Jayavelu, A. K. et al. The proteogenomic subtypes of acute myeloid leukemia. Cancer Cell 40, 301\u2013317.e12 (2022).","journal-title":"Cancer Cell"},{"key":"9156_CR186","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1038\/s41375-022-01796-7","volume":"37","author":"S Stratmann","year":"2023","unstructured":"Stratmann, S. et al. Proteogenomic analysis of acute myeloid leukemia associates relapsed disease with reprogrammed energy metabolism both in adults and children. Leukemia 37, 550\u2013559 (2023).","journal-title":"Leukemia"},{"key":"9156_CR187","doi-asserted-by":"publisher","first-page":"1466","DOI":"10.3390\/cancers12061466","volume":"12","author":"E Aaseb\u00f8","year":"2020","unstructured":"Aaseb\u00f8, E. et al. The progression of acute myeloid leukemia from first diagnosis to chemoresistant relapse: a comparison of proteomic and phosphoproteomic profiles. Cancers 12, 1466 (2020).","journal-title":"Cancers"},{"key":"9156_CR188","doi-asserted-by":"publisher","first-page":"1649","DOI":"10.1038\/s41375-023-01963-4","volume":"37","author":"ML Morales","year":"2023","unstructured":"Morales, M. L. et al. Posttranslational splicing modifications as a key mechanism in cytarabine resistance in acute myeloid leukemia. Leukemia 37, 1649\u20131659 (2023).","journal-title":"Leukemia"},{"key":"9156_CR189","doi-asserted-by":"publisher","first-page":"7655","DOI":"10.3390\/ijms23147655","volume":"23","author":"I Cela","year":"2022","unstructured":"Cela, I. et al. Proteomic investigation of the role of nucleostemin in nucleophosmin-mutated OCI-AML 3 cell line. Int. J. Mol. Sci. 23, 7655 (2022).","journal-title":"Int. J. Mol. Sci."},{"key":"9156_CR190","doi-asserted-by":"publisher","DOI":"10.1186\/s13148-022-01329-0","volume":"14","author":"T Aumer","year":"2022","unstructured":"Aumer, T. et al. Comprehensive comparison between azacytidine and decitabine treatment in an acute myeloid leukemia cell line. Clin. Epigenet. 14, 113 (2022).","journal-title":"Clin. Epigenet."},{"key":"9156_CR191","doi-asserted-by":"publisher","first-page":"1507","DOI":"10.1182\/blood.2019003654","volume":"136","author":"S Raffel","year":"2020","unstructured":"Raffel, S. et al. Quantitative proteomics reveals specific metabolic features of acute myeloid leukemia stem cells. Blood 136, 1507\u20131519 (2020).","journal-title":"Blood"},{"key":"9156_CR192","doi-asserted-by":"publisher","first-page":"101359","DOI":"10.1016\/j.xcrm.2023.101359","volume":"5","author":"JC Pino","year":"2024","unstructured":"Pino, J. C. et al. Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia. Cell Rep. Med. 5, 101359 (2024).","journal-title":"Cell Rep. Med."},{"key":"9156_CR193","doi-asserted-by":"publisher","DOI":"10.1126\/scisignal.abl7989","volume":"15","author":"F Pedicona","year":"2022","unstructured":"Pedicona, F. et al. Targeting the lysine-specific demethylase 1 rewires kinase networks and primes leukemia cells for kinase inhibitor treatment. Sci. Signal. 15, eabl7989 (2022).","journal-title":"Sci. Signal."},{"key":"9156_CR194","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201600089","volume":"17","author":"M Matondo","year":"2017","unstructured":"Matondo, M. et al. Determination of differentially regulated proteins upon proteasome inhibition in AML cell lines by the combination of large-scale and targeted quantitative proteomics. Proteomics 17, 1600089 (2017).","journal-title":"Proteomics"},{"key":"9156_CR195","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-53398-9","volume":"15","author":"Y Chen","year":"2024","unstructured":"Chen, Y. et al. Succinate dehydrogenase deficiency-driven succinate accumulation induces drug resistance in acute myeloid leukemia via ubiquitin-cullin regulation. Nat. Commun. 15, 9820 (2024).","journal-title":"Nat. Commun."},{"key":"9156_CR196","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-84708-6","volume":"11","author":"JM Kempf","year":"2021","unstructured":"Kempf, J. M. et al. Loss-of-function mutations in the histone methyltransferase EZH2 promote chemotherapy resistance in AML. Sci. Rep. 11, 5838 (2021).","journal-title":"Sci. Rep."},{"key":"9156_CR197","doi-asserted-by":"publisher","first-page":"602","DOI":"10.1016\/j.ccell.2016.03.015","volume":"29","author":"ER Lechman","year":"2016","unstructured":"Lechman, E. R. et al. miR-126 regulates distinct self-renewal outcomes in normal and malignant hematopoietic stem cells. Cancer Cell 29, 602\u2013606 (2016).","journal-title":"Cancer Cell"},{"key":"9156_CR198","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1038\/leu.2016.297","volume":"31","author":"B Xu","year":"2017","unstructured":"Xu, B., Zhao, Y., Wang, X., Gong, P. & Ge, W. MZH29 is a novel potent inhibitor that overcomes drug resistance FLT3 mutations in acute myeloid leukemia. Leukemia 31, 913\u2013921 (2017).","journal-title":"Leukemia"},{"key":"9156_CR199","doi-asserted-by":"publisher","first-page":"2141","DOI":"10.1158\/0008-5472.CAN-21-0548","volume":"82","author":"A Pfeiffer","year":"2022","unstructured":"Pfeiffer, A. et al. Phosphorylation of SHP2 at Tyr62 enables acquired resistance to SHP2 allosteric inhibitors in FLT3-ITD-driven AML. Cancer Res. 82, 2141\u20132155 (2022).","journal-title":"Cancer Res."},{"key":"9156_CR200","doi-asserted-by":"publisher","first-page":"2143","DOI":"10.3390\/cancers13092143","volume":"13","author":"M Hernandez-Valladares","year":"2021","unstructured":"Hernandez-Valladares, M. et al. Proteomic studies of primary acute myeloid leukemia cells derived from patients before and during disease-stabilizing treatment based on all-trans retinoic acid and valproic acid. Cancers 13, 2143 (2021).","journal-title":"Cancers"},{"key":"9156_CR201","doi-asserted-by":"publisher","first-page":"1080","DOI":"10.1182\/blood.2021012778","volume":"139","author":"TM Schnoeder","year":"2022","unstructured":"Schnoeder, T. M. et al. PLCG1 is required for AML1-ETO leukemia stem cell self-renewal. Blood 139, 1080\u20131097 (2022).","journal-title":"Blood"},{"key":"9156_CR202","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1038\/s41375-021-01393-0","volume":"36","author":"F Perner","year":"2022","unstructured":"Perner, F. et al. YBX1 mediates translation of oncogenic transcripts to control cell competition in AML. Leukemia 36, 426\u2013437 (2022).","journal-title":"Leukemia"},{"key":"9156_CR203","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/s41589-021-00742-5","volume":"17","author":"L Wang","year":"2021","unstructured":"Wang, L. et al. Discovery of a first-in-class CDK2 selective degrader for AML differentiation therapy. Nat. Chem. Biol. 17, 567\u2013575 (2021).","journal-title":"Nat. Chem. Biol."},{"key":"9156_CR204","doi-asserted-by":"publisher","first-page":"1818","DOI":"10.1038\/s41375-018-0032-1","volume":"32","author":"P Casado","year":"2018","unstructured":"Casado, P. et al. Proteomic and genomic integration identifies kinase and differentiation determinants of kinase inhibitor sensitivity in leukemia cells. Leukemia 32, 1818\u20131822 (2018).","journal-title":"Leukemia"},{"key":"9156_CR205","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1038\/leu.2017.284","volume":"32","author":"M-A Hospital","year":"2018","unstructured":"Hospital, M.-A. et al. RSK2 is a new Pim2 target with pro-survival functions in FLT3-ITD-positive acute myeloid leukemia. Leukemia 32, 597\u2013605 (2018).","journal-title":"Leukemia"},{"key":"9156_CR206","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31155-0","volume":"13","author":"L Liu","year":"2022","unstructured":"Liu, L. et al. The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors. Nat. Commun. 13, 3833 (2022).","journal-title":"Nat. Commun."},{"key":"9156_CR207","doi-asserted-by":"crossref","unstructured":"Ctortecka, C. et al. Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications. Nat. Commun. 15, 5707 (2024).","DOI":"10.1038\/s41467-024-49651-w"},{"key":"9156_CR208","doi-asserted-by":"publisher","unstructured":"Boussaid, Ismael. Rshiny Code used for \u2018Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia\u2019. Zenodo https:\/\/doi.org\/10.5281\/zenodo.17356461 (2025).","DOI":"10.5281\/zenodo.17356461"}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09156-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09156-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09156-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T10:02:40Z","timestamp":1765965760000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09156-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,17]]},"references-count":208,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["9156"],"URL":"https:\/\/doi.org\/10.1038\/s42003-025-09156-8","relation":{},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,17]]},"assertion":[{"value":"2 April 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 October 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 December 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1768"}}