Multiparameter functional diversity of human C2H2 zinc finger proteins

Genome Res. 2016 Dec;26(12):1742-1752. doi: 10.1101/gr.209643.116. Epub 2016 Nov 16.


C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether or how these proteins regulate transcription. Most of the ∼700 human C2H2-ZF proteins also contain at least one KRAB, SCAN, BTB, or SET domain, suggesting that they may have common interacting partners and/or effector functions. Here, we report a multifaceted functional analysis of 131 human C2H2-ZF proteins, encompassing DNA binding sites, interacting proteins, and transcriptional response to genetic perturbation. We confirm the expected diversity in DNA binding motifs and genomic binding sites, and provide motif models for 78 previously uncharacterized C2H2-ZF proteins, most of which are unique. Surprisingly, the diversity in protein-protein interactions is nearly as high as diversity in DNA binding motifs: Most C2H2-ZF proteins interact with a unique spectrum of co-activators and co-repressors. Thus, multiparameter diversification likely underlies the evolutionary success of this large class of human proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • CYS2-HIS2 Zinc Fingers
  • DNA / metabolism*
  • Evolution, Molecular
  • Gene Expression Regulation
  • HEK293 Cells
  • Humans
  • Protein Binding
  • Protein Interaction Maps
  • Sequence Analysis, DNA
  • Sequence Analysis, RNA
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism*


  • Transcription Factors
  • DNA