Extended supplementary data for manuscript: Specialised super-enhancer networks in stem cells and neurons

Super-enhancers (SEs) are clusters of enhancers with high transcriptional activity that play essential roles in defining cell identity through regulation of nearby genes. SEs are also known to form extensive multiway chromatin interactions in embryonic stem cells, which span tens of megabases with other SEs and highly transcribed regions. However, the properties and contributions of SEs in shaping complex regulatory interactions, and how they differ between dividing and in terminally differentiated cells remain poorly understood. Here, we study the structural and functional properties of SEs in embryonic stem cells and dopaminergic neurons by combining Genome Architecture Mapping (GAM), chromatin accessibility, histone modification, and transcriptome data. We find that most SEs are cell-type specific and form extensive pairwise and multiway chromatin interactions with differentially expressed genes and other SEs. SE interactions frequently connect topologically associating domains across megabase genomic distances. Cell-type specific SEs establish complex chromatin interactions with other SEs and highly transcribed regions. SE network analysis identifies important SEs, with highest centrality. Central SEs contain binding motifs for cell-type specific transcription factors, and may act as regulatory hubs. The functional heterogeneity of SEs is also highlighted by their organization into modular sub-networks that differ in structure and spatial scale between ESCs and DNs, with more specific and strongly connected SE modules in post-mitotic neurons. Our results uncover the complexity and specificity of SE-based 3D regulatory networks and provide a resource for prioritizing SEs with potential roles in transcriptional regulation and disease.