3S-DB identifies an RNA repository facilitating stop codon readthrough for selenocysteine insertion and selenoproteome expansion.

Chenfang Si, Lu Zhang, Jing Gao, Kongyan Niu, Yunxia Li, Nan Liu, Bing Shan, Yaoyang Zhang

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Article in Redox biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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8 authors.

Chenfang SiInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., Shanghai, 201210, China; The Core Facility Center, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.

Lu ZhangInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China.

Jing GaoInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., Shanghai, 201210, China.

Kongyan NiuInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., Shanghai, 201210, China.

Yunxia LiInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., Shanghai, 201210, China.

Nan LiuInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., Shanghai, 201210, China; Shanghai Key Laboratory of Aging Studies, 100 Haike Rd., Shanghai, 201210, China.

Bing ShanInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., Shanghai, 201210, China. Electronic address: shanbing@sioc.ac.cn.

Yaoyang ZhangInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., Shanghai, 201210, China; Shanghai Key Laboratory of Aging Studies, 100 Haike Rd., Shanghai, 201210, China. Electronic address: zyy@sioc.ac.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Selenoproteins contain the selenocysteine (Sec, U), which is essential for redox regulation due to its reactive selenol group. The current set of 25 human selenoproteins was defined by the presence of SECIS elements in the 3' UTR coupled with in-frame UGA codons through a stop codon readthrough mechanism. However, the discovery of novel selenoproteins and SECIS elements remains limited by the constraints of SECIS prediction methods. In this study, we focus on SECISBP2, the core SECIS-binding protein, to analyze its binding RNAs using RNA immunoprecipitation sequencing (RIP-Seq) technology. We constructed the 3S-DB, a database of 1,333 SECISBP2-bound RNAs with potential SECIS functions for UGA recoding, including most known selenoprotein transcripts. Importantly, we validate that the 3' UTRs of PDF and ATP5MJ exhibit SECIS activity using luciferase assays and by fusing them to known selenoprotein RNAs. In summary, our results provide a valuable resource of mRNAs with potential for UGA recoding and previously unrecognized SECIS elements, with the potential to expand the known selenoproteome and advance our understanding of their roles in redox biology and beyond. Furthermore, this work offers new insights into non-canonical stop codon readthrough and the broader mechanisms governing translational regulation of the genetic code.

Indexed as

Codon, TerminatorProteomeRNA-Binding ProteinsSelenocysteineSelenoproteins3' Untranslated RegionsHumans3' Untranslated RegionsCodon, TerminatorProteomeRNA-Binding ProteinsSECISBP2 protein, humanSelenocysteineSelenoproteinsRedox biologySECISSecMSSelenoproteinStop codon readthrough

Identifiers

PMID41201471

DOI10.1016/j.redox.2025.103888

PMCPMC12628022

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