title: A genome-wide map of CTCF multivalency redefines the CTCF code.
abstract: The "CTCF code" hypothesis posits that CTCF pleiotropic functions are driven by recognition of diverse sequences through combinatorial use of its 11 zinc fingers (ZFs). This model, however, is supported by in vitro binding studies of a limited number of sequences. To study CTCF multivalency in vivo, we define ZF binding requirements at ∼50,000 genomic sites in primary lymphocytes. We find that CTCF reads sequence diversity through ZF clustering. ZFs 4-7 anchor CTCF to ∼80% of targets containing the core motif. Nonconserved flanking sequences are recognized by ZFs 1-2 and ZFs 8-11 clusters, which also stabilize CTCF broadly. Alternatively, ZFs 9-11 associate with a second phylogenetically conserved upstream motif at ∼15% of its sites. Individually, ZFs increase overall binding and chromatin residence time. Unexpectedly, we also uncovered a conserved downstream DNA motif that destabilizes CTCF occupancy. Thus, CTCF associates with a wide array of DNA modules via combinatorial clustering of its 11 ZFs.
authors.affiliation: Genomics and Immunity, NIAMS.
authors.forename: Hirotaka
authors.initials: H
authors.lastname: Nakahashi
authors.affiliation: Genomics and Immunity, NIAMS.
authors.forename: Kyong-Rim
authors.initials: KR
authors.lastname: Kieffer Kwon
authors.affiliation: Genomics and Immunity, NIAMS.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Resch
authors.affiliation: Genomics and Immunity, NIAMS.
authors.forename: Laura
authors.initials: L
authors.lastname: Vian
authors.affiliation: Genomics and Immunity, NIAMS.
authors.forename: Marei
authors.initials: M
authors.lastname: Dose
authors.affiliation: Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Diana
authors.initials: D
authors.lastname: Stavreva
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
authors.forename: Ofir
authors.initials: O
authors.lastname: Hakim
authors.affiliation: Genomics and Immunity, NIAMS.
authors.forename: Nathanael
authors.initials: N
authors.lastname: Pruett
authors.affiliation: Genomics and Immunity, NIAMS.
authors.forename: Steevenson
authors.initials: S
authors.lastname: Nelson
authors.affiliation: Genomics and Immunity, NIAMS.
authors.forename: Arito
authors.initials: A
authors.lastname: Yamane
authors.affiliation: Genomics and Immunity, NIAMS.
authors.forename: Jason
authors.initials: J
authors.lastname: Qian
authors.affiliation: Center of Cancer Research, NCI.
authors.forename: Wendy
authors.initials: W
authors.lastname: Dubois
authors.affiliation: Peconic LLC, State College, PA 16803, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Welsh
authors.affiliation: Integrative Bioinformatics Inc., Mountain View, CA 94024, USA.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Phair
authors.affiliation: Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: B Franklin
authors.initials: BF
authors.lastname: Pugh
authors.affiliation: Laboratory of Immunopathology, NIAID, National Institutes of Health, Rockville, MD 20852, USA.
authors.forename: Victor
authors.initials: V
authors.lastname: Lobanenkov
authors.affiliation: Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Gordon L
authors.initials: GL
authors.lastname: Hager
authors.affiliation: Genomics and Immunity, NIAMS.|Center of Cancer Research, NCI.
authors.forename: Rafael
authors.initials: R
authors.lastname: Casellas
mesh_terms: D000818:Animals; D001402:B-Lymphocytes / Q000378:metabolism; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002874:Chromosome Mapping; D016678:Genome; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D059372:Nucleotide Motifs; D038761:Photobleaching; D012097:Repressor Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016335:Zinc Fingers / Q000235:genetics
chemical_list: D000076246:CCCTC-Binding Factor; C000619698:Ctcf protein, mouse; D012097:Repressor Proteins