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Slic-seq for A-to-I edited transcripts enrichment

ABSTRACT: Slic-seq for A-to-I edited transcripts enrichment

PROVIDER: PRJNA717743 | ENA |

REPOSITORIES: ENA

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Slic-seq for A-to-I edited transcripts enrichment

Project description:Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional processing event involved in diversifying the transcriptome responsible for various biological processes. In this context, we developed a new biochemical method that enriches the inosine-containing RNA. The objective is the accurate identification of A-to-I editing sites, eliminating false positives caused by RNA-DNA differences. This method was applied to three neurological diseases, demonstrating that A-to-I editing sites significantly decreased in neuronal activity genes.

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SLIC-CAGE (Super-Low Input Carrier-CAGE) development: comparison with Saccharomyces cerevisiae nAnTi-CAGE and nanoCAGE libraries and validation of SLIC-CAGE on Mus musculus total RNA

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Selective Enrichment of A-to-I Edited Transcripts from Cellular RNA Using Endonuclease V.

Project description:Creating accurate maps of A-to-I RNA editing activity is vital to improving our understanding of the biological role of this process and harnessing it as a signal for disease diagnosis. Current RNA sequencing techniques are susceptible to random sampling limitations due to the complexity of the transcriptome and require large amounts of RNA material, specialized instrumentation, and high read counts to accurately interrogate A-to-I editing sites. To address these challenges, we show that Escherichia coli Endonuclease V (eEndoV), an inosine-cleaving enzyme, can be repurposed to bind and isolate A-to-I edited transcripts from cellular RNA. While Mg2+ enables eEndoV to catalyze RNA cleavage, we show that similar levels of Ca2+ instead promote binding of inosine without cleavage and thus enable high affinity capture of inosine in RNA. We leverage this capability to demonstrate EndoVIPER-seq (Endonuclease V inosine precipitation enrichment sequencing) as a facile and effective method to enrich A-to-I edited transcripts prior to RNA-seq, producing significant increases in the coverage and detection of identified editing sites. We envision the use of this approach as a straightforward and cost-effective strategy to improve the epitranscriptomic informational density of RNA samples, facilitating a deeper understanding of the functional roles of A-to-I editing.

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