β-catenin links cell seeding density to global gene expression during mouse embryonic stem cell differentiation
Lucy LeBlanc,
Mijeong Kim,
Aparna Kambhampati,
Albert J. Son,
Nereida Ramirez,
Jonghwan Kim
Affiliations
Lucy LeBlanc
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA
Mijeong Kim
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA
Aparna Kambhampati
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; UT Southwestern Medical School, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
Albert J. Son
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
Nereida Ramirez
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
Jonghwan Kim
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA; Corresponding author
Summary: Although cell density is known to affect numerous biological processes including gene expression and cell fate specification, mechanistic understanding of what factors link cell density to global gene regulation is lacking. Here, we reveal that the expression of thousands of genes in mouse embryonic stem cells (mESCs) is affected by cell seeding density and that low cell density enhances the efficiency of differentiation. Mechanistically, β-catenin is localized primarily to adherens junctions during both self-renewal and differentiation at high density. However, when mESCs differentiate at low density, β-catenin translocates to the nucleus and associates with Tcf7l1, inducing co-occupied lineage markers. Meanwhile, Esrrb sustains the expression of pluripotency-associated genes while repressing lineage markers at high density, and its association with DNA decreases at low density. Our results provide new insights into the previously neglected but pervasive phenomenon of density-dependent gene regulation.
