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Background  Transcription factor (TF) binding to regulatory DNA sites is a key determinant of cell identity within multi-cellular organisms and has been studied extensively in relation to site affinity and chromatin modifications. There has been a strong focus on the inference of TF-gene regulatory networks and TF-TF physical interaction networks. Here, we present a third type of TF network, the spatial network of co-localized TF binding sites within the three-dimensional genome.    Results  Using published canonical Hi-C data and single-cell genome structures, we assess the spatial proximity of a genome-wide array of potential TF-TF co-localizations in human and mouse cell lines. For individual TFs, the abundance of occupied binding sites shows a positive correspondence with their clustering in three dimensions, and this is especially apparent for weak TF binding sites and at enhancer regions. An analysis between different TF proteins identifies significantly proximal pairs, which are enriched in reported physical interactions. Furthermore, clustering of different TFs based on proximity enrichment identifies two partially segregated co-localization sub-networks, involving different TFs in different cell types. Using data from both human lymphoblastoid cells and mouse embryonic stem cells, we find that these sub-networks are enriched within, but not exclusive to, different chromosome sub-compartments that have been identified previously in Hi-C data.    Conclusions  This suggests that the association of TFs within spatial networks is closely coupled to gene regulatory networks. This applies to both differentiated and undifferentiated cells and is a potential causal link between lineage-specific TF binding and chromosome sub-compartment segregation.    Electronic supplementary material  The online version of this article (10.1186/s13059-018-1558-2) contains supplementary material, which is available to authorized users.

Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors