Work

LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data

Year: 2024

Type: article

Abstract: RNA editing is a highly conserved process. Adenosine deaminase acting on RNA (ADAR) mediated deamination of adenosine (A-to-I editing) is associated with human disease and immune checkpoint control. Functional implications of A-to-I editing are currently of broad interest to academic and industrial research as underscored by the fast-growing number of clinical studies applying base editors as therapeutic tools. Analyzing the dynamics of A-to-I editing, in a biological or therapeutic context, requires the sensitive detection of differential A-to-I editing, a currently unmet need. We introduce the local differential editing index (LoDEI) to detect differential A-to-I editing in RNA-seq datasets using a sliding-window approach coupled with an empirical q value calculation that detects more A-to-I editing sites at the same false-discovery rate compared to existing methods. LoDEI is validated on known and novel datasets revealing that the oncogene MYCN increases and that a specific small non-coding RNA reduces A-to-I editing.

Source: Nature Communications

DOI: 10.1038/s41467-024-53298-y

Authors: Phillipp Torkler, Marina Sauer, Uwe Schwartz, Selim Corbacioglu, Gunhild Sommer, Tilman Heise

Institutions: Deggendorf Institute of Technology, University Hospital Regensburg, University of Regensburg

Language: English

Topic: RNA regulation and disease

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $6,790