Function and Evolution of C2H2 Zinc Finger Arrays

Abstract

Krüppel-type or C2H2 zinc fingers represent a dominant DNA-binding motif in eukaryotic transcription factor (TF) proteins. In Krüppel-type (KZNF) TFs, KZNF motifs are arranged in arrays of three to as many as 40 tandem units, which cooperate to define the unique DNA recognition properties of the protein. Each finger contains four amino acids located at specific positions, which are brought into direct contact with adjacent nucleotides in the DNA sequence as the KZNF array winds around the major groove of the alpha helix. This arrangement creates an intimate and potentially predictable relationship between the amino acid sequence of KZNF arrays and the nucleotide sequence of target binding sites. The large number of possible combinations and arrangements of modular KZNF motifs, and the increasing lengths of KZNF arrays in vertebrate species, has created huge repertoires of functionally unique TF proteins. The properties of this versatile DNA-binding motif have been exploited independently many times over the course of evolution, through attachment to effector motifs that confer activating, repressing or other activities to the proteins. Once created, some of these novel inventions have expanded in specific evolutionary clades, creating large families of TFs that are lineage- or species-unique. This chapter reviews the properties and their remarkable evolutionary history of eukaryotic KZNF TF proteins, with special focus on large families that dominate the TF landscapes in different metazoan species.

Multiparameter functional diversity of human C2H2 zinc finger proteins

“…In metazoans, C2H2-ZF proteins are well known for their diversification in DNA binding, and frequent association with a small number of effector domains (Stubbs et al 2011). Surprisingly, we find that the PPIs of human C2H2-ZF proteins are nearly as diverse as their DNA binding motifs and genomic binding sites, and can vary dramatically among proteins that share the same type of effector domain.…”

“…The sequence specificity of C2H2-ZF arrays appears to evolve utilizing several attributes of their modularity, including alteration of specificity residues and domain shuffling (Stubbs et al 2011). In addition, we find that different sets of C2H2-ZF domains are often employed among paralogs.…”

The C2H2-ZF transcription factor Zfp335 recognizes two consensus motifs using separate zinc finger arrays

“…N-terminal ZF sequence specificities mapped to individual motif 1 half-sites C2H2-ZFs typically function in arrays of three or more units that enable recognition of multinucleotide sequences (Stubbs et al 2011). The bipartite structure of motif 1, with its two well-defined half-sites separated by a spacer of constrained length, raised the possibility that these half-sites may be bound separately by distinct yet spatially linked ZF arrays.…”

“…C2H2-ZFs are often assembled in a modular fashion to form tandem arrays that concatenate individual ZF specificities to recognize longer sequences. The human genome encodes >700 C2H2-ZF proteins (Emerson and Thomas 2009), many of which are known to play important roles in development and disease, although the biological functions and sequence specificities of most family members remain poorly characterized (Stubbs et al 2011).…”

ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters

“…Among the roughly 2000 site-specific DNA-binding TFs, the C2H2 ZNFs are the largest class encoded in the human genome. Although the biological functions of the majority of ZNFs are unknown, the molecular functions of ZNFs include not only sequence-specific binding to DNA but also protein-protein interactions and RNA binding (Stubbs et al 2011;Najafabadi et al 2015). DNA-binding ZNFs generally have multiple, adjacent, properly spaced zinc fingers in their DNA binding domain; ZNFs with fewer than three properly spaced fingers are more likely to be involved in protein-protein or protein-RNA interactions (Brown 2005;Brayer and Segal 2008).…”