Time-resolved transcriptomics of FEN1 knockdown HEK293T cells identifies altered rhythmic gene expression

Circadian rhythms coordinate genome-wide transcriptional oscillations that contribute to cellular homeostasis. Although the molecular clock machinery has been extensively characterized, how circadian transcription interfaces with processes such as the DNA damage response and cell cycle regulation remains incompletely defined. In this study, we examined the potential involvement of the DNA replication and repair nuclease FEN1 in circadian-associated transcriptional dynamics in human cells. Using time-series RNA sequencing across six circadian time points in synchronized HEK293T cells, we observed that FEN1 knockdown was accompanied by notable changes in rhythmic gene expression patterns. Approximately 30% of oscillatory transcripts exhibited alterations in rhythmicity, including loss or gain of daily oscillation, phase shifts, or amplitude changes. Genes showing altered rhythmic properties were enriched in pathways related to cell cycle regulation, DNA damage response, and cellular senescence. Phase set enrichment analysis indicated coordinated phase delays or inversions among subsets of G1/S checkpoint regulators and metabolic genes, suggesting altered temporal organization. While rhythmic expression of core clock genes was largely preserved, changes in oscillation amplitude and phase were observed, consistent with modified rhythmic stability. In parallel, cell-based analyses revealed changes in cell cycle distribution, including reduced S-phase entry, accumulation in G1 phase, and increased markers of cellular senescence, in agreement with transcriptomic trends. Collectively, these observations indicate that FEN1 depletion is associated with altered circadian-related transcriptional patterns and concurrent changes in cell cycle and senescence-related processes, providing insight into potential links between genome maintenance pathways and temporal gene expression programs.