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

Area of Science:

• Molecular Biology
• Genetics
• Chronobiology

Background:

• Circadian rhythms regulate daily gene expression for cellular homeostasis.
• The interplay between circadian transcription and DNA damage response/cell cycle regulation is not fully understood.

Purpose of the Study:

• To investigate the role of the DNA replication and repair nuclease FEN1 in circadian transcriptional dynamics.
• To explore the connection between FEN1, genome maintenance, and temporal gene expression programs.

Main Methods:

• Time-series RNA sequencing in synchronized HEK293T cells across six circadian time points.
• FEN1 knockdown experiments to assess effects on gene expression rhythmicity.
• Cell-based analyses of cell cycle distribution and senescence markers.

Main Results:

• FEN1 knockdown altered rhythmicity in approximately 30% of oscillating transcripts, including phase shifts and amplitude changes.
• Genes with altered rhythmic properties were enriched in cell cycle regulation, DNA damage response, and senescence pathways.
• FEN1 depletion led to G1 phase accumulation, reduced S-phase entry, and increased senescence markers.

Conclusions:

• FEN1 plays a role in maintaining circadian transcriptional patterns and regulating cell cycle progression.
• Disruption of FEN1 impacts genome maintenance pathways and cellular temporal organization.
• This study provides insights into the links between DNA repair mechanisms and the circadian clock.