Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs.
Abstract
Endogenous uridine-rich small nuclear RNAs (U snRNAs) form RNA-protein complexes to process eukaryotic pre-mRNA into mRNA. Previous studies have demonstrated programmable U snRNA guide-targeted exon inclusion and exclusion. Here we investigated whether snRNAs can also enhance RNA base editing over state-of-the-art RNA-targeting technologies in human cells. Compared with adenosine deaminase acting on RNA (ADAR)-recruiting circular RNAs, we find that guided A>I snRNAs consistently increase adenosine-to-inosine editing for higher exon count genes, perturb substantially fewer off-target genes and localize more persistently to the nucleus where ADAR is expressed. A>I snRNAs also more efficiently edit long noncoding RNAs and pre-mRNA 3' splice sites to promote splicing changes. Lastly, snRNA-H/ACA box snoRNA fusions (U>Ψ snRNAs) increase targeted RNA pseudouridylation without DKC1 overexpression, facilitating improved CFTR rescue from nonsense-mediated mRNA decay in a cystic fibrosis human bronchial epithelial cell model. Our results advance the endogenous protein-mediated RNA base editing toolbox and RNA-targeting technologies to treat genetic diseases.
Linked Datasets (1)
Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs
Homo sapiens20 data files
| File | Type | Size |
|---|---|---|
| DMD_cad_rep1_S10_L001_R1_001.fastq.gz | RNA-Seq | 2.2 GB |
| DMD_cad_rep1_S10_L001_R1_001.fastq.gz | RNA-Seq | 2.2 GB |
| DMD_cad_rep3_S11_L001_R1_001.fastq.gz | RNA-Seq | 2.3 GB |
| DMD_cad_rep3_S11_L001_R1_001.fastq.gz | RNA-Seq | 2.3 GB |
| DMD_U7_rep2_S12_L001_R1_001.fastq.gz | RNA-Seq | 2.5 GB |
| DMD_U7_rep2_S12_L001_R1_001.fastq.gz | RNA-Seq | 2.5 GB |
| DMD_U7_rep3_S13_L001_R1_001.fastq.gz | RNA-Seq | 2.5 GB |
| DMD_U7_rep3_S13_L001_R1_001.fastq.gz | RNA-Seq | 2.5 GB |
| pUC19_rep1_S32_L001_R1_001.fastq.gz | RNA-Seq | 2.3 GB |
| pUC19_rep1_S32_L001_R1_001.fastq.gz | RNA-Seq | 2.3 GB |
| pUC19_rep2_S33_L001_R1_001.fastq.gz | RNA-Seq | 2.5 GB |
| pUC19_rep2_S33_L001_R1_001.fastq.gz | RNA-Seq | 2.5 GB |
| RAB7A_cad_rep1_S34_L001_R1_001.fastq.gz | RNA-Seq | 2.4 GB |
| RAB7A_cad_rep1_S34_L001_R1_001.fastq.gz | RNA-Seq | 2.4 GB |
| RAB7A_cad_rep2_S35_L001_R1_001.fastq.gz | RNA-Seq | 2.5 GB |
| RAB7A_cad_rep2_S35_L001_R1_001.fastq.gz | RNA-Seq | 2.5 GB |
| RAB7A_U7_rep2_S36_L001_R1_001.fastq.gz | RNA-Seq | 2.3 GB |
| RAB7A_U7_rep2_S36_L001_R1_001.fastq.gz | RNA-Seq | 2.3 GB |
| RAB7A_U7_rep3_S37_L001_R1_001.fastq.gz | RNA-Seq | 2.6 GB |
| RAB7A_U7_rep3_S37_L001_R1_001.fastq.gz | RNA-Seq | 2.6 GB |
Potentially Related Datasets (1)
These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.