PT  - JOURNAL ARTICLE
AU  - Claudia Cattoglio
AU  - Iryna Pustova
AU  - Jaclyn J. Ho
AU  - Carla J. Inouye
AU  - Gina M. Dailey
AU  - Xavier Darzacq
AU  - Robert Tjian
AU  - Anders S. Hansen
TI  - Architectural Features of 3D Genome Organization Revealed by Counting CTCF and Cohesin Molecules
AID  - 10.1101/370650
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 370650
4099  - http://biorxiv.org/content/early/2018/07/17/370650.short
4100  - http://biorxiv.org/content/early/2018/07/17/370650.full
AB  - Achieving a quantitative and predictive understanding of 3D genome architecture presents a major challenge and aspiration. However, this milestone will not be achieved without quantitative measurements of the key proteins driving nuclear organization. Here we report the quantification of CTCF and cohesin, two causal regulators of topological associating domains (TADs) in mammalian cells. Within the context of the cohesin/CTCF mediated loop extrusion model and recent imaging studies (Hansen 2017), here we determine the density of extruding cohesins and CTCF boundary permeability. Furthermore, co-immunoprecipitation studies of an endogenously tagged subunit (Rad21) confirms the presence of dimers and/or oligomers. Having established cell lines with accurately measured protein abundances, we report a simple method to conveniently count molecules of any Halo-tagged protein in the nucleus. We anticipate that these tools and results will advance a more quantitative understanding of 3D genome organization, and facilitate quantifying proteins involved in diverse biological processes.