Multiparameter functional diversity of human C2H2 zinc finger proteins

Abstract

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.

KRAB zinc finger proteins

“…Furthermore, although the length of KRAB-ZFPs (given the many ZNFs present in each array) should allow for a very high degree of specificity in the recognition of long DNA targets, it has been noted that KRAB-ZFP binding motifs are usually shorter than predicted. This suggests that different ZNFs in a KRAB-ZFP recognize different DNA motifs, as is the case for the C 2 H 2 ZNF protein CTCF (Nakahashi et al, 2013), or that ZNFs not involved in contacting DNA could engage in other types of interactions, for instance with RNA or proteins (Najafabadi et al, 2015;Imbeault et al, 2017;Schmitges et al, 2016). Some highly conserved KRAB-ZFPs contain additional elements in their N terminus, such as SCAN or DUF3669 domains.…”

“…Many promoter-binding KRAB-ZFPs are ancient and evolutionarily conserved, and contain SCAN or DUF3669 domains; most do not recruit KAP1 and, as yet, are of unknown function Schmitges et al, 2016). Some associate with wide arrays of promoters, for instance ZNF202, which binds in the vicinity of several thousand transcriptional start sites (TSSs).…”

“…2). Accordingly, many KRAB-ZFPs act as transcriptional repressors via the KAP1-nucleated induction of heterochromatin and, in early embryonic cells, via DNA methylation (Wolf and Goff, 2009;Quenneville et al, 2012;Rowe et al, 2013;Jacobs et al, 2014;Najafabadi et al, 2015;Ecco et al, 2016;Schmitges et al, 2016;Imbeault et al, 2017). However, not all KRAB-ZFPs bind KAP1, and the interactome of more ancient human family members, notably those endowed with SCAN or All KRAB-ZFPs contain a KRAB domain and an array of zinc fingers with DNA-binding potential, the sequence specificity of which is dictated mainly by three amino acids within each zinc finger (at positions 6, 3 and -1).…”

“…The genomic targets of a large fraction of human KRAB-ZFPs have been characterized in recent studies using chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and tagged proteins overexpressed in 293T cells as bait (Najafabadi et al, 2015;Imbeault et al, 2017;Schmitges et al, 2016). This type of analysis does not allow one to conclude which genomic locus or loci are bound by a KRAB-ZFP in the physiological setting of a particular cell, as its recruitment stands to be differentially affected by the presence of other DNA-binding proteins, by the state of the chromatin and perhaps by levels of DNA methylation at potential target loci.…”

“…Many of their roles involve KAP1, which binds to a sizeable fraction of human and murine KRAB-ZFPs (Schmitges et al, 2016). KAP1 acts as a scaffold for a silencing complex that comprises the histone methyltransferase SETDB1 (also known as ESET) (Schultz et al, 2002), the nucleosome remodeling and deacetylation (NuRD) complex (Schultz et al, 2001), heterochromatin protein 1 (HP1) (Nielsen et al, 1999;Sripathy et al, 2006) and DNA methyltransferases (Fig.…”