The dynamics of chromatin topology in human cells

Division Of Basic Sciences - Nci

Investigators

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Abstract

In FY 2022, we quantitatively characterized genome-wide DNA supercoiling patterns in human cells, with carefully designed control experiments to correct for the offset due to the readout of other factors. We then analyzed DNA supercoiling patterns in correlation with the 3D chromatin structure and histone marks, studied the potential players in establishing and maintaining such supercoiling patterns by perturbation experiments probing transcription, cohesin, and topoisomerase activities. The final goal is to elucidate the regulation mechanism and the biological function of DNA supercoiling in human cells. On the other hand, the fast dynamics of DNA supercoiling in living cells lead to a significant cell-to-cell variation, averaging out a significant portion of the meaningful signal. To address this challenge, we are synchronizing cell populations by a variety of approaches to allow better and more sensitive detection. We are also developing single-cell assays for DNA supercoiling, utilizing the principle of linear amplification derived from my previously developed LIANTI assay.