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Watch Chromatin “Breathe” in Embryonic Stem Cells

This holiday season, we breathed in lots of good smells—the scent of pine trees, the aroma of pumpkin pie, and the unmistakable smoky smell of a roaring fire. Now, researchers say they’ve caught chromatin in the act of “breathing” in human embryonic stem cells (hESCs) before they differentiate.

The team from California and Italy developed a new method for watching chromatin movements in real time in vivo.


The new tracking method rapidly scans in a line across fluorescently labeled chromatin. The researchers do this over and over to get a time series of chromatin intensity. They then do various mathematical tricks. Here’s what they found out:

  • In hESCs, chromatin moved back and forth (which they call “breathing”) at frequencies of 10 to 100 Hz. In HELA cells—which are differentiated but unregulated—the chromatin vibrated a whole lot less. However, the chromatin in regulated and differentiated NIH3T3 cells was very different—there were no peaks of movement.
  • From other experiments, it was clear that the movements were not due to whole cell movement or mechanical vibration—they really came from the chromatin.
  • The oscillations of chromatin movement in hESCs were energy-dependent.
  • As differentiation progressed in hESCs, the peaks of chromatin movement got smaller and smaller.

“We thus propose that the measured chromatin high frequency movements in hESCs may represent a hallmark of pluripotency and serve as a mechanism to maintain the genome in a transcriptionally accessible state,” they conclude.

So, does chromatin breathe? Read the paper at Epigenetics & Chromatin, December 2012.