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An attractive model to explore light input to the circadian clock in vertebrates is the zebrafish. Circadian clocks in zebrafish peripheral tissues and even zebrafish-derived cell lines are entrainable by direct light exposure thus providing unique insight into the function and evolution of light regulatory pathways. Our previous work has revealed that light-induced gene transcription is a key step in the entrainment of the circadian clock as well as enabling the more general adaptation of zebrafish cells to sunlight exposure. However, considerable evidence points to post-transcriptional regulatory mechanisms, notably microRNAs (miRNAs), playing an essential role in shaping dynamic changes in mRNA levels. Therefore, does light directly impact the function of miRNAs? Are there light-regulated miRNAs and if so, which classes of mRNA do they target? To address these questions, we performed a complete sequencing analysis of light-induced changes in the zebrafish transcriptome, encompassing small non-coding RNAs as well as mRNAs. Importantly, we identified sets of light-regulated miRNAs, with many regulatory targets representing light-inducible mRNAs including circadian clock genes and genes involved in redox homeostasis. We subsequently focused on the light-responsive miR-204-3-3p and miR-430a-3p which are predicted to regulate the expression of cryptochrome genes (<jats:italic>cry1a<\/jats:italic> and <jats:italic>cry1b<\/jats:italic>). Luciferase reporter assays validated the target binding of miR-204-3-3p and miR-430a-3p to the 3\u2032UTRs of <jats:italic>cry1a<\/jats:italic> and <jats:italic>cry1b<\/jats:italic>, respectively. Furthermore, treatment with mimics and inhibitors of these two miRNAs significantly affected the dynamic expression of their target genes but also other core clock components (<jats:italic>clock1a<\/jats:italic>, <jats:italic>bmal1b<\/jats:italic>, <jats:italic>per1b<\/jats:italic>, <jats:italic>per2<\/jats:italic>, <jats:italic>per3<\/jats:italic>), as well as the rhythmic locomotor activity of zebrafish larvae. Thus, our identification of light-responsive miRNAs reveals new intricacy in the multi-level regulation of the circadian clockwork by light.<\/jats:p>","DOI":"10.1371\/journal.pgen.1011545","type":"journal-article","created":{"date-parts":[[2025,1,8]],"date-time":"2025-01-08T19:34:42Z","timestamp":1736364882000},"page":"e1011545","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Light-regulated microRNAs shape dynamic gene expression in the zebrafish circadian 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