Hyomin Seo, Winston H. Cuddleston, Ting Fu, Elisa Navarro, Madison Parks et al.
Myeloid cells undergo large changes to their gene expression profile in response to inflammatory stimulation. This includes an increase in post-transcriptional modifications carried out by adenosine-to-inosine (A-to-I) and cytosine-to-uracil (C-to-U) RNA editing enzymes. However, the precise RNA editing targets altered by stimulation and the consequences of RNA editing on gene expression and the proteome have been understudied. We present a comprehensive RNA editing analysis of stimulated myeloid cells across three independent cohorts totalling 297 samples, including monocytes and IPS-derived microglia. We observed that C-to-U editing, while less abundant, has a higher effect size in response to stimulation than A-to-I, and has a greater potential to recode the proteome. We investigated the consequences of RNA editing on RNA stability and gene expression using in silico and in vitro reporter methods, and identified a recoding C-to-U site in ARSB that mimics a reported lysosomal storage disorder mutation.
Hyomin Seo, Winston H. Cuddleston, Ting Fu, Elisa Navarro, Madison Parks, Amanda Allan, Anastasia G. Efthymiou, Michael S. Breen, Xinshu Xiao, Towfique Raj, Jack Humphrey. Cytosine-to-uracil RNA editing is upregulated by pro-inflammatory stimulation of myeloid cells. 2025-03-17. https://doi.org/10.1101/2025.03.14.643382
A library of 164-bp 3′ UTR oligonucleotides carrying either the reference or RNA-edited nucleotide was cloned into a reporter vector and electroporated into HEK293T cells. Three biological replicates were assayed by reporter RNA sequencing and plasmid DNA sequencing, and MPRAnalyze was used to compare edited-versus-reference RNA/DNA abundance.
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