RT Journal Article
SR Electronic
T1 Substrate diversity of NSUN enzymes and links of 5-methylcytosine to mRNA translation and turnover
JF Life Science Alliance
JO Life Sci. Alliance
FD Life Science Alliance LLC
SP e202402613
DO 10.26508/lsa.202402613
VO 7
IS 9
A1 Guarnacci, Marco
A1 Zhang, Pei-Hong
A1 Kanchi, Madhu
A1 Hung, Yu-Ting
A1 Lin, Hanrong
A1 Shirokikh, Nikolay E
A1 Yang, Li
A1 Preiss, Thomas
YR 2024
UL https://www.life-science-alliance.org/content/7/9/e202402613.abstract
AB Maps of the RNA modification 5-methylcytosine (m5C) often diverge markedly not only because of differences in detection methods, data depth and analysis pipelines but also biological factors. We re-analysed bisulfite RNA sequencing datasets from five human cell lines and seven tissues using a coherent m5C site calling pipeline. With the resulting union list of 6,393 m5C sites, we studied site distribution, enzymology, interaction with RNA-binding proteins and molecular function. We confirmed tRNA:m5C methyltransferases NSUN2 and NSUN6 as the main mRNA m5C “writers,” but further showed that the rRNA:m5C methyltransferase NSUN5 can also modify mRNA. Each enzyme recognises mRNA features that strongly resemble their canonical substrates. By analysing proximity between mRNA m5C sites and footprints of RNA-binding proteins, we identified new candidates for functional interactions, including the RNA helicases DDX3X, involved in mRNA translation, and UPF1, an mRNA decay factor. We found that lack of NSUN2 in HeLa cells affected both steady-state levels of, and UPF1-binding to, target mRNAs. Our studies emphasise the emerging diversity of m5C writers and readers and their effect on mRNA function.All source code used during this study is available at https://github.com/YangLab/Epitranscriptomic-maps-of-5-methylcytosine. All raw and processed sequencing data generated in this study have been submitted to the NCBI Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE252369.