Profiling A-to-I RNA editing during mouse somatic reprogramming at the single-cell level

Lv, Tianhang; Jiang, Siyuan; Wang, Xiaoshan; Hou, Yong

doi:10.1016/j.heliyon.2023.e18133

Cited by 1 publication

(3 citation statements)

References 57 publications

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“…In this part, we first present theoretical evidence that insect cells are not favorable for constructing scRNA-Seq data and then provide statistical data to show that scRNA-Seq for insects is indeed very rare. We found that both strategies of scRNA-Seq inevitably have shortcomings in RNA editing detection, but bioinformaticians have devoted efforts to achieving this goal [55][56][57][58], and we can anticipate the broad application of RNA editing ideas to the scRNA-Seq data in the near future.…”

Section: Detecting Rna Editing In Single Cells Is Promising But Chall...mentioning

confidence: 99%

“…We found a few studies of RNA editing using scRNA-Seq [55][56][57][58], including three papers on humans [55][56][57] and one paper on mice [58], while no insect species were investigated. From these facts, we see a promising trend that researchers are trying to identify RNA editing events from the single-cell data, but the scarcity of relevant studies might reflect some unresolved technical limitations behind this idea, especially for nonmodel insects.…”

Section: Detecting Rna Editing In Single Cells Is Promising But Chall...mentioning

confidence: 99%

“…As mentioned above, the full-length mRNA strategy of scRNA-Seq suffers from limited reads per cell, jeopardizing the precise detection of RNA editing events. Nevertheless, bioinformatics aims to fully take advantage of existing data, and the full-length scRNA-Seq is already the best approach to help study RNA editing at the single-cell level [55][56][57][58]. Moreover, bulk RNA-Seq data accompanying the scRNA-Seq data are highly preferred.…”

Section: Detecting Rna Editing In Single Cells Is Promising But Chall...mentioning

confidence: 99%

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Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes

Xu,

Liu,

Zhao

et al. 2023

IJMS

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Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent RNA modification in the nervous systems of metazoans. To study the biological significance of RNA editing, we first have to accurately identify these editing events from the transcriptome. The genome-wide identification of RNA editing sites remains a challenging task. In this review, we will first introduce the occurrence, regulation, and importance of A-to-I RNA editing and then describe the established bioinformatic procedures and difficulties in the accurate identification of these sit esespecially in small sized non-model insects. In brief, (1) to obtain an accurate profile of RNA editing sites, a transcriptome coupled with the DNA resequencing of a matched sample is favorable; (2) the single-cell sequencing technique is ready to be applied to RNA editing studies, but there are a few limitations to overcome; (3) during mapping and variant calling steps, various issues, like mapping and base quality, soft-clipping, and the positions of mismatches on reads, should be carefully considered; (4) Sanger sequencing of both RNA and the matched DNA is the best verification of RNA editing sites, but other auxiliary evidence, like the nonsynonymous-to-synonymous ratio or the linkage information, is also helpful for judging the reliability of editing sites. We have systematically reviewed the understanding of the biological significance of RNA editing and summarized the methodology for identifying such editing events. We also raised several promising aspects and challenges in this field. With insightful perspectives on both scientific and technical issues, our review will benefit the researchers in the broader RNA editing community.

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Section: Detecting Rna Editing In Single Cells Is Promising But Chall...mentioning

confidence: 99%

Section: Detecting Rna Editing In Single Cells Is Promising But Chall...mentioning

confidence: 99%

Section: Detecting Rna Editing In Single Cells Is Promising But Chall...mentioning

confidence: 99%

See 1 more Smart Citation

Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes

Xu,

Liu,

Zhao

et al. 2023

IJMS

View full text Add to dashboard Cite

show abstract

Profiling A-to-I RNA editing during mouse somatic reprogramming at the single-cell level

Cited by 1 publication

References 57 publications

Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes

Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes

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