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Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs

ABSTRACT: Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs

PROVIDER: PRJNA1254645 | ENA |

REPOSITORIES: ENA

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Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs

Project description: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. We investigated whether snRNAs can also enhance RNA base editing over state-of-the-art RNA-targeting technologies in human cells. Compared to 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 lncRNAs and pre-mRNA 3′ splice sites to promote splicing changes. Finally, 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.

2025-07-03 | GSE295421 | GEO

Base editing improvement

Project description:Base editing improvement

| PRJNA598586 | ENA

Base Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

Project description:The study of 5-hydroxylmethylcytosines (5hmC), the sixth base of the mammalian genome, as an epigenetic mark has been hampered by a lack of method to map it at single-base resolution. Previous affinity purification-based methods could not precisely locate 5hmC nor accurately determine its relative abundance at each modified site. We here present a genome-wide approach for mapping 5hmC at base resolution. Application of this new method to the embryonic stem cells not only confirms widespread distribution of 5hmC in mammalian genome, but also reveals a strong sequence bias and strand asymmetry at sites of 5hmC. Additionally, the relative abundance of 5hmC varies significantly depending on the types of functional sequences, suggesting different mechanisms for 5hmC deposition and maintenance. Furthermore, we observe high levels of 5hmC and reciprocally low levels of 5mC at transcription factor binding sites, revealing a dynamic DNA methylation process at cis-regulatory elements. Base resolution sequencing of 5 hydroxymethylcytosine in human and mouse embryonic stem cells

2012-05-16 | E-GEOD-36173 | biostudies-arrayexpress

Base editing improvement

Project description:We examined the off-targets of new base editing tools at RNA level

2020-10-14 | GSE142840 | GEO

Base Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

2012-05-17 | GSE36173 | GEO

ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts.

Project description: Not available

| S-EPMC9852825 | biostudies-literature

Single-base resolution methylome of 5-methylcytosine in mammalian transcriptome

Project description:Single-base resolution methylome of 5-methylcytosine in mammalian transcriptome

| PRJNA301456 | ENA

Base Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

Project description:Base Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

| PRJNA156839 | ENA

Base editing in Agrobacteria

Project description:Efficient CRISPR-mediated base editing in Agrobacterium spp.

| PRJEB38304 | ENA

Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome

Project description:While DNA N6-methyl-deoxyadenosine (6mA) is abundant in bacteria and protists, its presence and function in mammalian genomes have been less clear. We present Direct-Read 6mA sequencing (DR-6mA-seq), an antibody-independent method to measure 6mA at base-resolution with high sensitivity. DR-6mA-seq employs a unique mutation-based strategy to reveal 6mA sites as misincorporation signatures without any chemical or enzymatic modulation of 6mA. We validated DR-6mA-seq through successful mapping of the well-characterized G(6mA)TC motif in the E. coli DNA and identified 6mA sites in the mammalian mitochondrial DNA. As expected, when applying DR-6mA-seq to mammalian systems, we found that genomic DNA (gDNA) 6mA abundance is in general low in most mammalian tissues and cells; however, we did observe distinct gDNA 6mA sites in mouse testis and glioblastoma cells. DR-6mA-seq provides an enabling tool to detect 6mA at single-base resolution with high sensitivity for a comprehensive understanding of DNA 6mA in eukaryotes.

2023-12-28 | GSE213876 | GEO

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