TY - JOUR TI - Determining cellular CTCF and cohesin abundances to constrain 3D genome models AU - Cattoglio, Claudia AU - Pustova, Iryna AU - Walther, Nike AU - Ho, Jaclyn J AU - Hantsche-Grininger, Merle AU - Inouye, Carla J AU - Hossain, M Julius AU - Dailey, Gina M AU - Ellenberg, Jan AU - Darzacq, Xavier AU - Tjian, Robert AU - Hansen, Anders S A2 - Sherratt, David J A2 - Struhl, Kevin A2 - Sherratt, David J VL - 8 PY - 2019 DA - 2019/06/17 SP - e40164 C1 - eLife 2019;8:e40164 DO - 10.7554/eLife.40164 UR - https://doi.org/10.7554/eLife.40164 AB - Achieving a quantitative and predictive understanding of 3D genome architecture remains a major challenge, as it requires quantitative measurements of the key proteins involved. Here, we report the quantification of CTCF and cohesin, two causal regulators of topologically associating domains (TADs) in mammalian cells. Extending our previous imaging studies (Hansen et al., 2017), we estimate bounds on the density of putatively DNA loop-extruding cohesin complexes and CTCF binding site occupancy. Furthermore, co-immunoprecipitation studies of an endogenously tagged subunit (Rad21) suggest the presence of cohesin dimers and/or oligomers. Finally, based on our cell lines with accurately measured protein abundances, we report a method to conveniently determine the number of molecules of any Halo-tagged protein in the cell. We anticipate that our results and the established tool for measuring cellular protein abundances will advance a more quantitative understanding of 3D genome organization, and facilitate protein quantification, key to comprehend diverse biological processes. KW - CTCF KW - cohesin KW - loop extrusion KW - TAD KW - genome organization KW - Rad21 JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -