A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code
Hirotaka Nakahashi,
Kyong-Rim Kieffer Kwon,
Wolfgang Resch,
Laura Vian,
Marei Dose,
Diana Stavreva,
Ofir Hakim,
Nathanael Pruett,
Steevenson Nelson,
Arito Yamane,
Jason Qian,
Wendy Dubois,
Scott Welsh,
Robert D. Phair,
B. Franklin Pugh,
Victor Lobanenkov,
Gordon L. Hager,
Rafael Casellas
Affiliations
Hirotaka Nakahashi
Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
Kyong-Rim Kieffer Kwon
Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
Wolfgang Resch
Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
Laura Vian
Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
Marei Dose
Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
Diana Stavreva
Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
Ofir Hakim
The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
Nathanael Pruett
Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
Steevenson Nelson
Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
Arito Yamane
Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
Jason Qian
Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
Wendy Dubois
Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
Scott Welsh
Peconic LLC, State College, PA 16803, USA
Robert D. Phair
Integrative Bioinformatics Inc., Mountain View, CA 94024, USA
B. Franklin Pugh
Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
Victor Lobanenkov
Laboratory of Immunopathology, NIAID, National Institutes of Health, Rockville, MD 20852, USA
Gordon L. Hager
Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
Rafael Casellas
Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
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.
