Cell 149, 1447–1460 (2012)

Histone modifications are thought to regulate gene expression by altering chromatin structure. Hathaway et al. now report a method that allows them to establish epigenetic roles and inheritance patterns for histone marks in living cells. Their 'chromatin in vivo assay' (CiA) system builds on the principle of 'chemically induced proximity', in which a small molecule with two distinct protein-binding domains acts as a scaffold to reversibly bring proteins into proximity. In the CiA system, small molecules were used to localize chromatin-active proteins to the Oct4 promoter of mouse embryonic stem cells or somatic cells. Rapamycin-mediated localization of heterochromatin protein 1 (HP1α)—a factor known to interact with enzymes that trimethylate Lys9 of histone H3 (H3K9me3)—initiated trimethylation of H3K9 repressed Oct4 gene expression. Prolonged HP1α recruitment resulted in stabilized Oct4 repression as a consequence of H3K9me3 spreading and DNA methylation at the promoter. Rapamycin washout allowed the authors to test epigenetic memory and established that the H3K9me3 mark is stably inherited across multiple cell passages. Similarly, targeting of the transcriptional activator VP12 to the Oct4 promoter by abscissic acid–mediated dimerization revealed that strongly activating complexes could override repressed chromatin states. Integrated with a kinetic modeling approach developed by the authors, the CiA system offers a powerful quantitative approach for inducing specific chromatin states in cells and dissecting the dynamic roles of histone modifications in gene expression regulation.