Prostate cancer is increasingly recognized as a disease influenced not only by genetic and molecular alterations but also by disruption of circadian regulatory networks. Advances in RNA sequencing (RNA-Seq) have enabled transcriptome-wide investigation of temporal gene expression patterns, revealing complex interactions between core clock genes, androgen receptor signaling, alternative splicing, and metabolic pathways. Emerging evidence suggests that circadian dysregulation contributes to prostate cancer progression through alterations in gene expression, transcript isoform remodeling, and treatment resistance mechanisms. In particular, RNA-Seq studies have provided new insights into the relationship between clock gene networks and androgen receptor signaling, as well as the potential role of alternative splicing in the development of aggressive disease phenotypes. Recent bioinformatic approaches have further enabled the analysis of temporal patterns within large transcriptomic datasets lacking time-of-collection information. These advances have generated growing interest in chronotherapy, in which treatment timing may be optimized according to biological rhythms. Although clinical implementation remains limited, circadian transcriptomics offers a promising framework for understanding prostate cancer biology and developing more individualized therapeutic strategies. This review summarizes current evidence regarding circadian regulation in prostate cancer, with particular emphasis on RNA-Seq-derived insights into clock gene networks, transcriptome oscillations, alternative splicing, and potential chronotherapeutic applications.
