title: Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response.
abstract: Mammalian cells have developed intricate mechanisms to interpret, integrate, and respond to extracellular stimuli. For example, tumor necrosis factor (TNF) rapidly activates proinflammatory genes, but our understanding of how this occurs against the ongoing transcriptional program of the cell is far from complete. Here, we monitor the early phase of this cascade at high spatiotemporal resolution in TNF-stimulated human endothelial cells. NF-κB, the transcription factor complex driving the response, interferes with the regulatory machinery by binding active enhancers already in interaction with gene promoters. Notably, >50% of these enhancers do not encode canonical NF-κB binding motifs. Using a combination of genomics tools, we find that binding site selection plays a key role in NF-κΒ-mediated transcriptional activation and repression. We demonstrate the latter by describing the synergy between NF-κΒ and the corepressor JDP2. Finally, detailed analysis of a 2.8-Mbp locus using sub-kbp-resolution targeted chromatin conformation capture and genome editing uncovers how NF-κΒ that has just entered the nucleus exploits pre-existing chromatin looping to exert its multimodal role. This work highlights the involvement of topology in cis-regulatory element function during acute transcriptional responses, where primary DNA sequence and its higher-order structure constitute a regulatory context leading to either gene activation or repression.
authors.affiliation: Department of Cell Biology, Erasmus Medical Centre, 3015 CN Rotterdam, The Netherlands.
authors.forename: Petros
authors.initials: P
authors.lastname: Kolovos
authors.affiliation: Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany.
authors.forename: Theodore
authors.initials: T
authors.lastname: Georgomanolis
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, United Kingdom.
authors.forename: Anna
authors.initials: A
authors.lastname: Koeferle
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, United Kingdom.
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Larkin
authors.affiliation: Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany.
authors.forename: Lilija
authors.initials: L
authors.lastname: Brant
authors.affiliation: Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany.
authors.forename: Miloš
authors.initials: M
authors.lastname: Nikolicć
authors.affiliation: IZKF Computational Biology Research Group, RWTH Aachen University Medical School, 52062 Aachen, Germany.
authors.forename: Eduardo G
authors.initials: EG
authors.lastname: Gusmao
authors.affiliation: Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany.
authors.forename: Anne
authors.initials: A
authors.lastname: Zirkel
authors.affiliation: Department of Cell Biology, Erasmus Medical Centre, 3015 CN Rotterdam, The Netherlands.
authors.forename: Tobias A
authors.initials: TA
authors.lastname: Knoch
authors.affiliation: Center for Biomics, Erasmus Medical Centre, 3015 GE Rotterdam, The Netherlands.
authors.forename: Wilfred F
authors.initials: WF
authors.lastname: van Ijcken
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, United Kingdom.
authors.forename: Peter R
authors.initials: PR
authors.lastname: Cook
authors.affiliation: IZKF Computational Biology Research Group, RWTH Aachen University Medical School, 52062 Aachen, Germany.
authors.forename: Ivan G
authors.initials: IG
authors.lastname: Costa
authors.affiliation: Department of Cell Biology, Erasmus Medical Centre, 3015 CN Rotterdam, The Netherlands.
authors.forename: Frank G
authors.initials: FG
authors.lastname: Grosveld
authors.affiliation: Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany.
authors.forename: Argyris
authors.initials: A
authors.lastname: Papantonis
mesh_terms: D002478:Cells, Cultured; D002843:Chromatin / Q000378:metabolism; D016384:Consensus Sequence; D000072669:Gene Editing; D061307:Human Umbilical Vein Endothelial Cells / Q000187:drug effects / Q000378:metabolism; D006801:Humans; D007249:Inflammation / Q000235:genetics / Q000378:metabolism; D016328:NF-kappa B / Q000235:genetics / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D015533:Transcriptional Activation; D014409:Tumor Necrosis Factor-alpha / Q000494:pharmacology
chemical_list: D002843:Chromatin; C491387:JDP2 protein, human; D016328:NF-kappa B; D012097:Repressor Proteins; D014409:Tumor Necrosis Factor-alpha