[ad_1]
Krawczak, M., Ball, E. V. & Cooper, D. N. Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes. Am. J. Hum. Genet. 63, 474–488 (1998).
Mort, M., Ivanov, D., Cooper, D. N. & Chuzhanova, N. A. A meta-analysis of nonsense mutations causing human genetic disease. Hum. Mutat. 29, 1037–1047 (2008).
Cheng, S. H. et al. Defective intracellular transport and processing of CFTR is the molecular basis of most cystic fibrosis. Cell 63, 827–834 (1990).
Ballabio, A. & Gieselmann, V. Lysosomal disorders: from storage to cellular damage. Biochim. Biophys. Acta. 1793, 684–696 (2009).
Howard, M., Frizzell, R. A. & Bedwell, D. M. Aminoglycoside antibiotics restore CFTR function by overcoming premature stop mutations. Nat. Med. 2, 467–469 (1996).
Welch, E. M. et al. PTC124 targets genetic disorders caused by nonsense mutations. Nature 447, 87–91 (2007).
Dabrowski, M., Bukowy-Bieryllo, Z. & Zietkiewicz, E. Advances in therapeutic use of a drug-stimulated translational readthrough of premature termination codons. Mol. Med. 24, 25 (2018).
Lueck, J. D. et al. Engineered transfer RNAs for suppression of premature termination codons. Nat. Commun. 10, 822 (2019).
Wang, J. et al. AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice. Nature 604, 343–348 (2022).
Albers, S. et al. Engineered tRNAs suppress nonsense mutations in cells and in vivo. Nature 618, 842–848 (2023).
Temple, G. F., Dozy, A. M., Roy, K. L. & Kan, Y. W. Construction of a functional human suppressor tRNA gene: an approach to gene therapy for β-thalassaemia. Nature 296, 537–540 (1982).
Kiselev, A. V. et al. Suppression of nonsense mutations in the Dystrophin gene by a suppressor tRNA gene. Mol. Biol. (Mosk). 36, 43–47 (2002).
Cox, D. B. T. et al. RNA editing with CRISPR–Cas13. Science 358, 1019–1027 (2017).
Merkle, T. et al. Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides. Nat. Biotechnol. 37, 133–138 (2019).
Qu, L. et al. Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs. Nat. Biotechnol. 37, 1059–1069 (2019).
Katrekar, D. et al. In vivo RNA editing of point mutations via RNA-guided adenosine deaminases. Nat. Methods 16, 239–242 (2019).
Vogel, P. et al. Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs. Nat. Methods 15, 535–538 (2018).
Huang, X. et al. Programmable C-to-U RNA editing using the human APOBEC3A deaminase. EMBO J. 39, e104741 (2020).
Abudayyeh, O. O. et al. A cytosine deaminase for programmable single-base RNA editing. Science 365, 382–386 (2019).
Rauch, S. et al. Programmable RNA-guided RNA effector proteins built from human parts. Cell 178, 122–134 (2019).
Reautschnig, P. et al. CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo. Nat. Biotechnol. 40, 759–768 (2022).
Yi, Z. et al. Engineered circular ADAR-recruiting RNAs increase the efficiency and fidelity of RNA editing in vitro and in vivo. Nat. Biotechnol. 40, 946–955 (2022).
Katrekar, D. et al. Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs. Nat. Biotechnol. 40, 938–945 (2022).
Xu, C. et al. Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes. Nat. Methods 18, 499–506 (2021).
Kannan, S. et al. Compact RNA editors with small Cas13 proteins. Nat. Biotechnol. 40, 194–197 (2022).
Song, J. et al. CRISPR-free, programmable RNA pseudouridylation to suppress premature termination codons. Mol. Cell 83, 139–155 (2023).
Adachi, H. et al. Targeted pseudouridylation: an approach for suppressing nonsense mutations in disease genes. Mol. Cell 83, 637–651 (2023).
Montes, M. & Martinez, N. M. Rewriting the message: harnessing RNA pseudouridylation to tackle disease. Mol. Cell 83, 503–506 (2023).
Karijolich, J. & Yu, Y. T. Converting nonsense codons into sense codons by targeted pseudouridylation. Nature 474, 395–398 (2011).
Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997).
Geslain, R. & Pan, T. Functional analysis of human tRNA isodecoders. J. Mol. Biol. 396, 821–831 (2010).
Zhang, M. et al. Quantitative profiling of pseudouridylation landscape in the human transcriptome. Nat. Chem. Biol. 19, 1185–1195 (2023).
Kotha, K. & Clancy, J. P. Ivacaftor treatment of cystic fibrosis patients with the G551D mutation: a review of the evidence. Ther. Adv. Respir. Dis. 7, 288–296 (2013).
Kerem, E. Pharmacologic therapy for stop mutations: how much CFTR activity is enough? Curr. Opin. Pulm. Med. 10, 547–552 (2004).
Bunge, S. et al. Genotype-phenotype correlations in mucopolysaccharidosis type I using enzyme kinetics, immunoquantification and in vitro turnover studies. Biochim. Biophys. Acta 1407, 249–256 (1998).
Oussoren, E. et al. Residual α-L-iduronidase activity in fibroblasts of mild to severe Mucopolysaccharidosis type I patients. Mol. Genet. Metab. 109, 377–381 (2013).
Sun, H., Li, K., Liu, C. & Yi, C. Regulation and functions of non-m(6)A mRNA modifications. Nat. Rev. Mol. Cell Biol. 24, 714–731 (2023).
Kierzek, E. et al. The contribution of pseudouridine to stabilities and structure of RNAs. Nucleic Acids Res. 42, 3492–3501 (2014).
Keeling, K. M., Xue, X., Gunn, G. & Bedwell, D. M. Therapeutics based on stop codon readthrough. Annu. Rev. Genomics Hum. Genet. 15, 371–394 (2014).
McClain, W. H., Foss, K., Jenkins, R. A. & Schneider, J. Nucleotides that determine Escherichia coli tRNA(Arg) and tRNA(Lys) acceptor identities revealed by analyses of mutant opal and amber suppressor tRNAs. Proc. Natl Acad. Sci. USA 87, 9260–9264 (1990).
Giege, R. & Eriani, G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res. 51, 1528–1570 (2023).
Pechmann, S. & Frydman, J. Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. Nat. Struct. Mol. Biol. 20, 237–243 (2013).
Porter, J. J., Heil, C. S. & Lueck, J. D. Therapeutic promise of engineered nonsense suppressor tRNAs. Wiley Interdiscip. Rev. RNA 12, e1641 (2021).
Eyler, D. E. et al. Pseudouridinylation of mRNA coding sequences alters translation. Proc. Natl Acad. Sci. USA 116, 23068–23074 (2019).
Prakash, T. P. et al. Targeted delivery of antisense oligonucleotides to hepatocytes using triantennary N-acetyl galactosamine improves potency 10-fold in mice. Nucleic Acids Res. 42, 8796–8807 (2014).
Zheng, G. et al. Efficient and quantitative high-throughput tRNA sequencing. Nat. Methods 12, 835–837 (2015).
Li, X. et al. Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. Nat. Chem. Biol. 12, 311–316 (2016).
Lu, B. et al. Transposase-assisted tagmentation of RNA/DNA hybrid duplexes. eLife 9, e54919 (2020).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).
Putri, G. H., Anders, S., Pyl, P. T., Pimanda, J. E. & Zanini, F. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics 38, 2943–2945 (2022).
Eisenberg, E. & Levanon, E. Y. Human housekeeping genes, revisited. Trends Genet. 29, 569–574 (2013).
Hounkpe, B. W., Chenou, F., de Lima, F. & De Paula, E. V. HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets. Nucleic Acids Res. 49, D947–D955 (2021).
Smith, T., Heger, A. & Sudbery, I. UMI-tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy. Genome Res. 27, 491–499 (2017).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962 (2016).
Luo, N. et al. Near-cognate tRNAs increase the efficiency and precision of pseudouridine-mediated readthrough of premature termination codons. GEO. www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237633 (2024).
Maqvi News #Maqvi #Maqvinews #Maqvi_news #Maqvi#News #info@maqvi.com
[ad_2]
Source link