title: Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus.
abstract: Higher order chromatin structures across the genome are maintained in part by the architectural proteins CCCTC binding factor (CTCF) and the cohesin complex, which co-localize at many sites across the genome. Here, we examine the role of these proteins in mediating chromatin structure at the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR encompasses nearly 200 kb flanked by CTCF-binding enhancer-blocking insulator elements and is regulated by cell-type-specific intronic enhancers, which loop to the promoter in the active locus. SiRNA-mediated depletion of CTCF or the cohesin component, RAD21, showed that these two factors have distinct roles in regulating the higher order organization of CFTR. CTCF mediates the interactions between CTCF/cohesin binding sites, some of which have enhancer-blocking insulator activity. Cohesin shares this tethering role, but in addition stabilizes interactions between the promoter and cis-acting intronic elements including enhancers, which are also dependent on the forkhead box A1/A2 (FOXA1/A2) transcription factors (TFs). Disruption of the three-dimensional structure of the CFTR gene by depletion of CTCF or RAD21 increases gene expression, which is accompanied by alterations in histone modifications and TF occupancy across the locus, and causes internalization of the gene from the nuclear periphery.
authors: Human Molecular Genetics Program, Lurie Children's Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
authors: Nehal
authors: N
authors: Gosalia
authors: Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60614, USA.
authors: Daniel
authors: D
authors: Neems
authors: Human Molecular Genetics Program, Lurie Children's Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
authors: Jenny L
authors: JL
authors: Kerschner
authors: Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60614, USA.
authors: Steven T
authors: ST
authors: Kosak
authors: Human Molecular Genetics Program, Lurie Children's Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA ann-harris@northwestern.edu.
authors: Ann
authors: A
authors: Harris
mesh_terms: D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D018938:Caco-2 Cells; D018797:Cell Cycle Proteins / Q000037:antagonists & inhibitors / Q000378:metabolism* / Q000502:physiology; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry*; D002868:Chromosomal Proteins, Non-Histone / Q000037:antagonists & inhibitors / Q000378:metabolism* / Q000502:physiology; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000235:genetics* / Q000378:metabolism; D005786:Gene Expression Regulation; D056426:Genetic Loci; D051541:Hepatocyte Nuclear Factor 3-alpha / Q000378:metabolism; D051542:Hepatocyte Nuclear Factor 3-beta / Q000378:metabolism; D006801:Humans; D012097:Repressor Proteins / Q000037:antagonists & inhibitors / Q000378:metabolism* / Q000502:physiology; D000097722:Cohesins
chemical_list: D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D019005:Cystic Fibrosis Transmembrane Conductance Regulator; D051541:Hepatocyte Nuclear Factor 3-alpha; D051542:Hepatocyte Nuclear Factor 3-beta; D012097:Repressor Proteins; D000097722:Cohesins; C000619697:CTCF protein, human