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eLife Assessment: Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing

Year: 2025
Type: peer-review
Abstract: eLife AssessmentThis potentially useful study introduces an orthogonal approach for detecting RNA modification, without chemical modification of RNA, which often results in RNA degradation and therefore loss of information.Compared to previous versions, the most recent one is improved and sufficiently aligned with the standards of the field to merit consideration by the research community, making the evidence solid according to said standards.Nevertheless, uncertainty regarding false positive and false negative rates remains, as it does for some of the alternative approaches.With more rigorous validation, the approach might be of particular interest for sites in RNA molecules where modifications are rare.Abstract 5-Methylcytosine (m 5 C) is one of the posttranscriptional modifications in mRNA and is involved in the pathogenesis of various diseases.However, the capacity of existing assays for accurately and comprehensively transcriptome-wide m 5 C mapping still needs improvement.Here, we develop a detection method named DRAM (deaminase and reader protein assisted RNA methylation analysis), in which deaminases (APOBEC1 and TadA-8e) are fused with m 5 C reader proteins (ALYREF and YBX1) to identify the m 5 C sites through deamination events neighboring the methylation sites.This antibody-free and bisulfite-free approach provides transcriptome-wide editing regions which are highly overlapped with the publicly available bisulfite-sequencing (BS-seq) datasets and allows for a more stable and comprehensive identification of the m 5 C loci.In addition, DRAM system even supports ultralow input RNA (10 ng).We anticipate that the DRAM system could pave the way for uncovering further biological functions of m 5 C modifications.
Source: eLife
DOI: 10.7554/elife.98166.5.sa0
Language: English
Open Access status: gold
Estimated APC paid: $2,500
OpenAlex ID: W4409267425
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