Temporal dynamics and functional annotation of transcriptome rhythmicity in HEK293T cells.
Level 5 - mechanism / opinion, no new human data
In vitro bench study (cell line transcriptomics).
PubMed 41746989 · doi:10.1371/journal.pone.0343991
What was done
The authors synchronized HEK293T cells and performed RNA sequencing at 13 time points over a 48-hour time course. They evaluated global transcriptome dynamics, replicate divergence, circadian rhythmicity of canonical clock and global genes, and pathway enrichment for both rhythmic and arrhythmic time-dependent transcripts.
What was found
Principal component analysis showed time-dependent separation, but coefficient of variation analysis demonstrated substantial divergence among biological replicates beginning at 28 hours (T28). Canonical core clock genes showed no detectable circadian rhythmicity when extending analysis past 28 hours. Only 785 expressed genes exhibited rhythmic expression across the genome, enriched for cytoskeletal/membrane structures, cytoplasmic/nuclear compartments, GTPase activator activity, and metal ion binding. Additionally, 645 arrhythmic genes displayed time-dependent expression enriched in G alpha signaling and chromatin structure pathways.
Why it matters
Because HEK293T cells are widely used as model systems, establishing that they have weak intrinsic circadian rhythmicity and substantial replicate divergence after 28 hours provides a crucial baseline reference for designing and interpreting time-sensitive experiments.
Limits
The study is restricted entirely to an immortalized in vitro cell line (HEK293T) and does not reflect primary human tissue biology. The abstract does not report the number of biological replicates (n), specific synchronization method, or exact statistical thresholds used to define rhythmicity, and it lacks protein or functional validation.
Cited by
- supports Over 15% of the human protein-coding genome is regulated by the circadian rhythm.