Spatial Organization of Regulatory Chromatin At Transcription Condensates*

Many biomolecular condensates associate with specific chromatin loci in the cell nucleus. Transcription condensates in mouse embryonic stem cells are thought to form at super-enhancer chromatin domains that are characterized by extended accumulations of transcription factor and coactivator binding sites. Bulk assays suggest that active chromatin marks are required for transcription condensate homeostasis. We uncover the epigenetic fingerprints of chromatin at transcription condensates below the diffraction limit with 3D multicolor single molecule super-resolution microscopy. Our results show general enrichment of nucleosomal chromatin inside transcription condensates and divergent spatial profiles of histone modifications associated with distinct types of chromatin regulatory elements. We link these findings to sequential stages of the transcription process. In particular, condensates appear to be foci of transcription initiation. Our findings begin to elucidate structure-function relationships of condensates in transcription regulation.