HP1ß has distinct subnuclear localizations, chromatin binding features and functions in embryonic stem cells and differentiating cells [ChIP-seq]

In recent years, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, although the role of the major heterochromatin proteins in pluripotency remains largely unknown. Here we identify heterochromatin protein 1-beta (HP1ß) to be differentially localized and associated with chromatin in pluripotent and differentiated cells, to be essential for proper ESC differentiation as well as for the maintenance of the pluripotent state. Microscopy analysis supported by biochemical fractionations and chromatin immunoprecipitation (ChIP) experiments demonstrate that unlike its prominent localization in heterochromatic chromocenters in differentiated cells, HP1ß is diffuse in the ESC nucleoplasm, poorly bound to chromatin, and highly expressed. The fraction of HP1ß that does associate with chromatin in ESCs is highly enriched in genic regions. HP1ß-knockout ESCs but not HP1a knockout ESCs exhibit a loss of the morphological and proliferative characteristics of embryonic pluripotent cells. HP1ß depletion in ESCs results in reduced expression of pluripotency factors and aberrant differentiation. In contrast, HP1ß depletion in differentiated cells perturbs the maintenance of differentiation, and facilitates reprogramming to induced pluripotent stem cells. Our results demonstrate a dual role for HP1ß, in ESCs it is essential for pluripotency maintenance, and in differentiated cells for proper differentiation. Overall design: ChIP-Seq of HP1ß in mouse embryonic stem cells.