Temporal dynamics and functional annotation of transcriptome rhythmicity in HEK293T cells

Area of Science:

• Cellular Biology
• Genomics
• Chronobiology

Background:

• The endogenous circadian clock regulates rhythmic cellular processes in humans.
• The temporal organization of the transcriptome in HEK293T cells is not fully understood.

Purpose of the Study:

• To map the transcriptome dynamics of synchronized HEK293T cells over a 48-hour cycle.
• To identify rhythmic and time-dependent gene expression patterns in HEK293T cells.

Main Methods:

• HEK293T cells were synchronized and subjected to RNA sequencing at 13 time points over 48 hours.
• Principal component analysis and coefficient of variation analyses were used to assess transcriptome dynamics and replicate variability.
• Genome-wide analysis identified rhythmic and arrhythmic gene expression patterns.

Main Results:

• Global transcriptomes showed time-dependent separation, but replicate divergence increased after 28 hours.
• Only 785 genes exhibited circadian rhythmicity, enriched in specific cellular compartments and molecular functions.
• 645 arrhythmic genes displayed time-dependent expression, enriched in pathways like G alpha signaling and chromatin structure.

Conclusions:

• HEK293T cells demonstrate weak intrinsic circadian transcriptome rhythmicity.
• The majority of transcripts in HEK293T cells remain time-independent within a 48-hour window.
• This dataset provides a reference for distinguishing time-dependent from time-independent gene regulation in HEK293T cells.