title: A pathway-centric view of spatial proximity in the 3D nucleome across cell lines.
abstract: In various contexts, spatially proximal genes have been shown to be functionally related. However, the extent to which spatial proximity of genes in a pathway contributes to the pathway's context-specific activity is not known. Leveraging Hi-C data in six human cell-lines, we show that spatial proximity of genes in a pathway is highly correlated with the pathway's context-specific expression and function. Furthermore, spatial proximity of pathway genes correlates with interactions of their protein products, and the specific pathway genes that are proximal to one another tend to occupy higher levels in the regulatory hierarchy. In addition to intra-pathway proximity, related pathways are spatially proximal to one another and housekeeping-genes tend to be proximal to several other pathways suggesting their coordinating role. Substantially extending previous works, our study reveals a pathway-centric organization of 3D-nucleome, whereby, functionally related interacting driver genes tend to be in spatial-proximity in a context-specific manner.
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
authors.forename: Hiren
authors.initials: H
authors.lastname: Karathia
authors.affiliation: Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
authors.forename: Carl
authors.initials: C
authors.lastname: Kingsford
authors.affiliation: Department of Physics, University of Maryland, College Park, MD, USA.
authors.forename: Michelle
authors.initials: M
authors.lastname: Girvan
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
authors.forename: Sridhar
authors.initials: S
authors.lastname: Hannenhalli
mesh_terms: D002460:Cell Line; D002843:Chromatin; D002875:Chromosomes / Q000648:ultrastructure*; D019295:Computational Biology; D030541:Databases, Genetic; D053595:Embryonic Stem Cells / Q000166:cytology; D004843:Epistasis, Genetic; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D015894:Genome, Human; D057809:HEK293 Cells; D006801:Humans; D008957:Models, Genetic; D025941:Protein Interaction Mapping; D015398:Signal Transduction; D012984:Software
chemical_list: D002843:Chromatin