title: Analysis of long-range interactions in primary human cells identifies cooperative CFTR regulatory elements.
abstract: A mechanism by which control DNA elements regulate transcription over large linear genomic distances is by achieving close physical proximity with genes, and looping of the intervening chromatin paths. Alterations of such regulatory 'chromatin looping' systems are likely to play a critical role in human genetic disease at large. Here, we studied the spatial organization of a ≈790 kb locus encompassing the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Dysregulation of CFTR is responsible for cystic fibrosis, which is the most common lethal genetic disorder in Caucasian populations. CFTR is a relatively large gene of 189 kb with a rather complex tissue-specific and temporal expression profile. We used chromatin conformation at the CFTR locus to identify new DNA sequences that regulate its transcription. By comparing 5C chromatin interaction maps of the CFTR locus in expressing and non-expressing human primary cells, we identified several new contact points between the CFTR promoter and its surroundings, in addition to regions featuring previously described regulatory elements. We demonstrate that two of these novel interacting regions cooperatively increase CFTR expression, and suggest that the new enhancer elements located on either side of the gene are brought together through chromatin looping via CTCF.
authors.affiliation: Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France.
authors.forename: Stéphanie
authors.identifier: http://orcid.org/0000-0001-7461-6076
authors.initials: S
authors.lastname: Moisan
authors.affiliation: Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada.
authors.forename: Soizik
authors.initials: S
authors.lastname: Berlivet
authors.affiliation: Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France.
authors.forename: Chandran
authors.initials: C
authors.lastname: Ka
authors.affiliation: Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France.
authors.forename: Gérald
authors.initials: G
authors.lastname: Le Gac
authors.affiliation: Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada josee.dostie@mcgill.ca.
authors.forename: Josée
authors.initials: J
authors.lastname: Dostie
authors.affiliation: Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France josee.dostie@mcgill.ca.
authors.forename: Claude
authors.initials: C
authors.lastname: Férec
mesh_terms: D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism; D003550:Cystic Fibrosis / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D004847:Epithelial Cells / Q000166:cytology / Q000378:metabolism; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D056426:Genetic Loci; D064368:Healthy Volunteers; D006801:Humans; D009296:Nasal Cavity / Q000166:cytology / Q000378:metabolism; D061251:Primary Cell Culture; D011401:Promoter Regions, Genetic; D012867:Skin / Q000166:cytology / Q000473:pathology; D014158:Transcription, Genetic
chemical_list: C505032:CFTR protein, human; D002843:Chromatin; D019005:Cystic Fibrosis Transmembrane Conductance Regulator