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| Status |
Public on Jan 29, 2024 |
| Title |
Near-cognate tRNAs increase the efficiency and precision of pseudouridine-mediated readthrough of premature termination codons [Target-seq] |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
Expression profiling by high throughput sequencing
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| Summary |
Nonsense mutations, responsible for ~11% of genetic diseases, create premature stop codons (PTCs) and lead to truncated and often non-functional proteins. Recently, programmable RNA pseudouridylation has emerged as a new type of RNA base editor to suppress PTCs. However, current methods suffer from low efficiency and limited precision. Here, we develop RESTART v3, an updated version of RESTART, which utilizes near-cognate tRNAs to improve the readthrough efficiency of pseudouridine-modified PTCs. We show an average of ~5-fold higher editing efficiency than RESTART v2 in cultured cells, currently the most active RNA pseudouridylation tool to mediate PTC readthrough. Moreover, RESTART v3 achieves functional PTC readthrough in disease cell models of cystic fibrosis and Hurler syndrome. Furthermore, RESTART v3 enables accurate incorporation of the original amino acid for nearly half of the PTC sites, considering the naturally occurring frequencies of sense to nonsense codons. In line with the benign off-target effect of RESTART, RESTART v3 does not change the coding information nor the expression level of transcripts with off-target editing; except for the specifically overexpressed tRNA molecule, it does not alter the expression level of endogenous tRNA pool. Overall, RESTART v3 represents an enhanced RNA base editor with increased efficiency and accuracy.
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| Overall design |
we examined the modification level of the PTC sites in HEK293T under the three versions of the RESTART system to evaluate the modification influence of near-cognate tRNAs
we examined the modification level of the PTC sites in 16HBE and MEF under the action of RESTART v3 system to evaluate the modification efficiency.
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| Web link |
https://www.nature.com/articles/s41587-024-02165-8
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| Citation(s) |
38448662 |
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| Submission date |
Jul 18, 2023 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Wenqing Liu |
| E-mail(s) |
puyulwq@163.com, liuwq21@gamils.com
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| Organization name |
Peking University
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| Street address |
No. 5 Summer Palace Road, Haidian District, Beijing
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| City |
Beijing |
| ZIP/Postal code |
010-100871 |
| Country |
China |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (27)
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| GSM7634959 |
HEK293T,RESTART v2-target TGA,rep 2 |
| GSM7634960 |
HEK293T,RESTART v3-target TGA,rep 1 |
| GSM7634961 |
HEK293T,RESTART v3-target TGA,rep 2 |
| GSM7634962 |
HEK293T,RESTART v1-target TAG,rep 1 |
| GSM7634963 |
HEK293T,RESTART v1-target TAG,rep 2 |
| GSM7634964 |
HEK293T,RESTART v2-target TAG,rep 1 |
| GSM7634965 |
HEK293T,RESTART v2-target TAG,rep 2 |
| GSM7634966 |
HEK293T,RESTART v3-target TAG,rep 1 |
| GSM7634967 |
HEK293T,RESTART v3-target TAG,rep 2 |
| GSM7634968 |
HEK293T,RESTART v1-target TAA,rep 1 |
| GSM7634969 |
HEK293T,RESTART v1-target TAA,rep 2 |
| GSM7634970 |
HEK293T,RESTART v2-target TAA,rep 1 |
| GSM7634971 |
HEK293T,RESTART v2-target TAA,rep 2 |
| GSM7634972 |
HEK293T,RESTART v3-target TAA,rep 1 |
| GSM7634973 |
HEK293T,RESTART v3-target TAA,rep 2 |
| GSM7634974 |
HEK293T,18S,rep1 |
| GSM7962130 |
16HBE, 18S, rep 1 |
| GSM7962131 |
16HBE, 18S, rep 2 |
| GSM7962132 |
16HBE, RESTART v3-treated, rep 1 |
| GSM7962133 |
16HBE, RESTART v3-treated, rep 2 |
| GSM7962134 |
16HBE, untreated, rep 1 |
| GSM7962135 |
MEF, RESTART v3-treated, rep 1 |
| GSM7962136 |
MEF, RESTART v3-treated, rep 2 |
| GSM7962137 |
MEF, untreated, rep 1 |
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| This SubSeries is part of SuperSeries: |
| GSE237633 |
Near-cognate tRNAs increase the efficiency and precision of pseudouridine-mediated readthrough of premature termination codons |
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| Relations |
| BioProject |
PRJNA996067 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE237629_Target_seq.results.xlsx |
10.8 Kb |
(ftp)(http) |
XLSX |
| GSE237629_targetseq-CFTRandmIDUA.xlsx |
10.1 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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