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Parallel Measurement of Circadian Clock Gene Expression and Hormone Secretion in Human Primary Cell Cultures
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Temporal dynamics and functional annotation of transcriptome rhythmicity in HEK293T cells.

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The human circadian clock influences cell processes, but HEK293T cell transcriptome rhythms are unclear. This study reveals limited circadian transcriptome rhythmicity in HEK293T cells, with most genes showing time-independent expression.

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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.