A genome-wide map of CTCF multivalency redefines the CTCF code

Cell Rep. 2013 May 30;3(5):1678-1689. doi: 10.1016/j.celrep.2013.04.024. Epub 2013 May 23.


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.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • B-Lymphocytes / metabolism
  • Binding Sites
  • CCCTC-Binding Factor
  • Chromosome Mapping
  • Genome*
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Nucleotide Motifs
  • Photobleaching
  • Repressor Proteins / chemistry
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*
  • Zinc Fingers / genetics


  • CCCTC-Binding Factor
  • Ctcf protein, mouse
  • Repressor Proteins

Associated data

  • GEO/GSE33819