Whole-transcriptome insights into light-responsive non-coding RNA networks regulating circadian clock and DNA repair in zebrafish

Light is a fundamental environmental cue that orchestrates a wide range of biological processes, from behavioral rhythms to molecular signaling pathways. Although the effects of light on entraining circadian clock and DNA repair have been well established, the post-transcriptional mechanisms involved in these responses are still not fully understood. In particular, the role of non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), in light-regulated gene expression remains unclear. Using light-responsive whole-transcriptome RNA sequencing of zebrafish larvae, we identified 1,365 differentially expressed (DE) mRNAs, 66 DE miRNAs, 330 DE lncRNAs, and 71 DE circRNAs. RT-qPCR analyses validated the expression changes of representative transcripts. Subsequently, by integrating mRNA and ncRNA datasets, we constructed a light-responsive competing endogenous RNA (ceRNA) network, which suggested extensive miRNA-mediated interactions among coding and non-coding RNA. Additional cis- and trans-regulatory network analyses uncovered potential regulatory relationships between ncRNAs and light-responsive genes. Functional enrichment analyses of target genes highlighted key pathways, including circadian rhythm, steroid biosynthesis, phototransduction, and oxidative stress response. Subnetwork analyses further identified ncRNA-mediated regulatory networks converging on circadian clock and DNA repair. Overall, our results suggest that light exposure induces a complex post-transcriptional regulatory network in zebrafish larvae. These findings contribute to our understanding of how ncRNAs function within the circadian clock and DNA repair systems, and advance the molecular basis of light-dependent gene regulation in vertebrates.