title: Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.
abstract: Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act in isolation of other interacting partners that also influence their impact. Indeed, the influence of multi-loci interactions remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these. Here we present a method that uses standard 4C-seq data to identify multi-loci interactions from the same cell. We demonstrate the feasibility of our method using 4C-seq data sets that identify known pairwise and novel tri-loci interactions involving the Tcrb and Igk antigen receptor enhancers. We further show that the three Igk enhancers, MiEκ, 3'Eκ and Edκ, interact simultaneously in this super-enhancer cluster, which add to our previous findings showing that loss of one element decreases interactions between all three elements as well as reducing their transcriptional output. These findings underscore the functional importance of simultaneous interactions and provide new insight into the relationship between enhancer elements. Our method opens the door for studying multi-loci interactions and their impact on gene regulation in other biological settings.
authors.affiliation: Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA.
authors.forename: Tingting
authors.initials: T
authors.lastname: Jiang
authors.affiliation: Department of Pathology, New York University School of Medicine, New York, NY, USA Department of Biology, New York University, New York, NY, USA.
authors.forename: Ramya
authors.initials: R
authors.lastname: Raviram
authors.affiliation: Department of Pathology, New York University School of Medicine, New York, NY, USA.
authors.forename: Valentina
authors.initials: V
authors.lastname: Snetkova
authors.affiliation: Department of Pathology, New York University School of Medicine, New York, NY, USA.
authors.forename: Pedro P
authors.initials: PP
authors.lastname: Rocha
authors.affiliation: Department of Pathology, New York University School of Medicine, New York, NY, USA.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Proudhon
authors.affiliation: Department of Pathology, New York University School of Medicine, New York, NY, USA Department of Biology, New York University, New York, NY, USA.
authors.forename: Sana
authors.initials: S
authors.lastname: Badri
authors.affiliation: Department of Biology, New York University, New York, NY, USA Department of Computer Science, Courant Institute of Mathematical Sciences, New York, NY, USA Simons Center for Data Analysis, New York, NY 10010, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Bonneau
authors.affiliation: Department of Pathology, New York University School of Medicine, New York, NY, USA jane.skok@med.nyu.edu.
authors.forename: Jane A
authors.initials: JA
authors.lastname: Skok
authors.affiliation: Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA Department of Pathology and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA Program of Applied Mathematics, Yale university, New Haven, CT, USA yuval.kluger@yale.edu.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Kluger
mesh_terms: D002843:Chromatin / Q000378:metabolism; D002875:Chromosomes / Q000378:metabolism*; D004742:Enhancer Elements, Genetic; D047629:Estrogen Receptor beta / Q000378:metabolism; D056426:Genetic Loci; D016678:Genome; D009690:Nucleic Acid Conformation; D016693:Receptors, Antigen, T-Cell, alpha-beta; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D002843:Chromatin; D047629:Estrogen Receptor beta; D016693:Receptors, Antigen, T-Cell, alpha-beta