Cell
Volume 184, Issue 4, 18 February 2021, Pages 1047-1063.e23
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Theory
Recording of elapsed time and temporal information about biological events using Cas9

https://doi.org/10.1016/j.cell.2021.01.014Get rights and content
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Highlights

  • CRISPR-Cas9 induces exponential decay of intact target frequency in cells over time

  • Elapsed time can be estimated from the observed intact target frequency

  • Multiple target sequences can be used for recording a wide range of times

  • The estimated time after biological events can also be recorded

Summary

DNA has not been utilized to record temporal information, although DNA has been used to record biological information and to compute mathematical problems. Here, we found that indel generation by Cas9 and guide RNA can occur at steady rates, in contrast to typical dynamic biological reactions, and the accumulated indel frequency can be a function of time. By measuring indel frequencies, we developed a method for recording and measuring absolute time periods over hours to weeks in mammalian cells. These time-recordings were conducted in several cell types, with different promoters and delivery vectors for Cas9, and in both cultured cells and cells of living mice. As applications, we recorded the duration of chemical exposure and the lengths of elapsed time since the onset of biological events (e.g., heat exposure and inflammation). We propose that our systems could serve as synthetic “DNA clocks.”

Keywords

DNA
clock
Cas9
CRISPR
time
temporal information
biological events
exponential decay
indel
elapsed time
timer

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