Ingolia, N. T. et al. Ribosome profiling reveals pervasive translation outdoors of annotated protein-coding genes. Cell Rep. 8, 1365–1379 (2014).
Ji, Z., Track, R., Regev, A. & Struhl, Ok. Many lncRNAs, 5′UTRs, and pseudogenes are translated and a few are prone to specific useful proteins. eLife 4, e08890 (2015).
Weatheritt, R. J., Sterne-Weiler, T. & Blencowe, B. J. The ribosome-engaged panorama of other splicing. Nat. Struct. Mol. Biol. 23, 1117–1123 (2016).
Sudmant, P. H., Lee, H., Dominguez, D., Heiman, M. & Burge, C. B. Widespread accumulation of ribosome-associated remoted 3′ UTRs in neuronal cell populations of the getting older mind. Cell Rep. 25, 2447–2456 e2444 (2018).
Adusumalli, S., Ngian, Z. Ok., Lin, W. Q., Benoukraf, T. & Ong, C. T. Elevated intron retention is a post-transcriptional signature related to progressive getting older and Alzheimer’s illness. Getting old Cell 18, e12928 (2019).
Mazin, P. et al. Widespread splicing adjustments in human mind improvement and getting older. Mol. Syst. Biol. 9, 633 (2013).
Hsieh, Y. C. et al. Tau-mediated disruption of the spliceosome triggers cryptic RNA splicing and neurodegeneration in Alzheimer’s illness. Cell Rep. 29, 301–316.e310 (2019).
Dvinge, H. & Bradley, R. Ok. Widespread intron retention diversifies most most cancers transcriptomes. Genome Med. 7, 45 (2015).
Lee, S. H. et al. Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia. Nature 561, 127–131 (2018).
Dhamija, S. et al. A pan-cancer evaluation reveals nonstop extension mutations inflicting SMAD4 tumour suppressor degradation. Nat. Cell Biol. 22, 999–1010 (2020).
Laumont, C. M. et al. Noncoding areas are the primary supply of targetable tumor-specific antigens. Sci. Transl. Med. 10, eaau5516 (2018).
Xiang, R. et al. Elevated expression of peptides from non-coding genes in most cancers proteomics datasets suggests potential tumor neoantigens. Commun. Biol. 4, 496 (2021).
Good, A. C. et al. Intron retention is a supply of neoepitopes in most cancers. Nat. Biotechnol. 36, 1056–1058 (2018).
Vakirlis, N. et al. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat. Commun. 11, 781 (2020).
Carvunis, A. R. et al. Proto-genes and de novo gene beginning. Nature 487, 370–374 (2012).
Yordanova, M. M. et al. AMD1 mRNA employs ribosome stalling as a mechanism for molecular reminiscence formation. Nature 553, 356–360 (2018).
Hashimoto, S., Nobuta, R., Izawa, T. & Inada, T. Translation arrest as a protein high quality management system for aberrant translation of the three′-UTR in mammalian cells. FEBS Lett. 593, 777–787 (2019).
Arribere, J. A. et al. Translation readthrough mitigation. Nature 534, 719–723 (2016).
Kramarski, L. & Arbely, E. Translational read-through promotes aggregation and shapes cease codon identification. Nucleic Acids Res. 48, 3747–3760 (2020).
Chen, J. et al. Pervasive useful translation of noncanonical human open studying frames. Science 367, 1140–1146 (2020).
van Heesch, S. et al. The translational panorama of the human coronary heart. Cell 178, 242–260.e229 (2019).
Djebali, S. et al. Panorama of transcription in human cells. Nature 489, 101–108 (2012).
Bai, B. et al. U1 small nuclear ribonucleoprotein advanced and RNA splicing alterations in Alzheimer’s illness. Proc. Natl Acad. Sci. USA 110, 16562–16567 (2013).
Wang, L. et al. SF3B1 and different novel most cancers genes in power lymphocytic leukemia. N. Engl. J. Med. 365, 2497–2506 (2011).
Hsu, T. Y. et al. The spliceosome is a therapeutic vulnerability in MYC-driven most cancers. Nature 525, 384–388 (2015).
Wang, D. et al. Inhibition of nonsense-mediated RNA decay by the tumor microenvironment promotes tumorigenesis. Mol. Cell. Biol. 31, 3670–3680 (2011).
Son, H. G. et al. RNA surveillance by way of nonsense-mediated mRNA decay is essential for longevity in daf-2/insulin/IGF-1 mutant C. elegans. Nat. Commun. 8, 14749 (2017).
Solar, Y., Eshov, A., Zhou, J., Isiktas, A. U. & Guo, J. U. C9orf72 arginine-rich dipeptide repeats inhibit UPF1-mediated RNA decay by way of translational repression. Nat. Commun. 11, 3354 (2020).
Wangen, J. R. & Inexperienced, R. Cease codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides. eLife 9, e52611 (2020).
Dong, C. et al. Intron retention-induced neoantigen load correlates with unfavorable prognosis in a number of myeloma. Oncogene 40, 6130–6138 (2021).
Lin, H. C. et al. C-terminal end-directed protein elimination by CRL2 ubiquitin ligases. Mol. Cell 70, 602–613.e603 (2018).
Koren, I. et al. The eukaryotic proteome is formed by E3 ubiquitin ligases concentrating on C-terminal degrons. Cell 173, 1622–1635.e1614 (2018).
Dyson, H. J. & Wright, P. E. Intrinsically unstructured proteins and their features. Nat. Rev. Mol. Cell Biol. 6, 197–208 (2005).
Zhang, Y. E., Vibranovski, M. D., Landback, P., Marais, G. A. B. & Lengthy, M. Y. Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene acquire on the X chromosome. PLoS Biol. 8, e1000494 (2010).
Wolfenden, R. V., Cullis, P. M. & Southgate, C. C. Water, protein folding, and the genetic code. Science 206, 575–577 (1979).
Juszkiewicz, S. & Hegde, R. S. Initiation of high quality management throughout poly(A) translation requires site-specific ribosome ubiquitination. Mol. Cell 65, 743–750 e744 (2017).
Liu, Z. et al. Systematic comparability of 2A peptides for cloning multi-genes in a polycistronic vector. Sci Rep. 7, 2193 (2017).
Wang, T., Wei, J. J., Sabatini, D. M. & Lander, E. S. Genetic screens in human cells utilizing the CRISPR–Cas9 system. Science 343, 80–84 (2014).
Wunderley, L., Leznicki, P., Payapilly, A. & Excessive, S. SGTA regulates the cytosolic high quality management of hydrophobic substrates. J. Cell Sci. 127, 4728–4739 (2014).
Shao, S., Rodrigo-Brenni, M. C., Kivlen, M. H. & Hegde, R. S. Mechanistic foundation for a molecular triage response. Science 355, 298–302 (2017).
Hessa, T. et al. Protein concentrating on and degradation are coupled for elimination of mislocalized proteins. Nature 475, 394–397 (2011).
Mariappan, M. et al. A ribosome-associating issue chaperones tail-anchored membrane proteins. Nature 466, 1120–1124 (2010).
Rodrigo-Brenni, M. C., Gutierrez, E. & Hegde, R. S. Cytosolic high quality management of mislocalized proteins requires RNF126 recruitment to Bag6. Mol. Cell 55, 227–237 (2014).
Hu, X. et al. RNF126-mediated reubiquitination is required for proteasomal degradation of p97-extracted membrane proteins. Mol. Cell 79, 320–331.e329 (2020).
Wang, Q. et al. A ubiquitin ligase-associated chaperone holdase maintains polypeptides in soluble states for proteasome degradation. Mol. Cell 42, 758–770 (2011).
Leznicki, P. & Excessive, S. SGTA associates with nascent membrane protein precursors. EMBO Rep. 21, e48835 (2020).
Akahane, T., Sahara, Ok., Yashiroda, H., Tanaka, Ok. & Murata, S. Involvement of Bag6 and the TRC pathway in proteasome meeting. Nat. Commun. 4, 2234 (2013).
Yewdell, J. W. & Nicchitta, C. V. The DRiP speculation decennial: assist, controversy, refinement and extension. Developments Immunol. 27, 368–373 (2006).
Minami, R. et al. BAG-6 is important for selective elimination of faulty proteasomal substrates. J. Cell Biol. 190, 637–650 (2010).
Huang, L., Kuhls, M. C. & Eisenlohr, L. C. Hydrophobicity as a driver of MHC class I antigen processing. EMBO J. 30, 1634–1644 (2011).
Brinkman, E. Ok., Chen, T., Amendola, M. & van Steensel, B. Straightforward quantitative evaluation of genome enhancing by sequence hint decomposition. Nucleic Acids Res. 42, e168 (2014).
Hezroni, H. et al. Rules of lengthy noncoding RNA evolution derived from direct comparability of transcriptomes in 17 species. Cell Rep. 11, 1110–1122 (2015).
Tareen, A. & Kinney, J. B. Logomaker: lovely sequence logos in Python. Bioinformatics 36, 2272–2274 (2020).
Joung, J. et al. Genome-scale CRISPR–Cas9 knockout and transcriptional activation screening. Nat. Protoc. 12, 828–863 (2017).
Li, W. et al. MAGeCK permits sturdy identification of important genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 15, 554 (2014).
Moffat, L. & Jones, D. T. Rising the accuracy of single sequence prediction strategies utilizing a deep semi-supervised studying framework. Bioinformatics 37, 3744–3751 (2021).
Osorio, D., Rondon-Villarreal, P. & Torres, R. Peptides: a bundle for knowledge mining of antimicrobial peptides. R J. 7, 4–14 (2015).
Miyazawa, S. & Jernigan, R. L. Estimation of efficient interresidue contact energies from protein crystal constructions: quasi-chemical approximation. Macromolecules 18, 534–552 (1985).
Lu, S. et al. CDD/SPARCLE: the conserved area database in 2020. Nucleic Acids Res. 48, D265–D268 (2020).