Deep Vertebrate Roots for Mammalian Zinc Finger Transcription Factor Subfamilies

Abstract

While many vertebrate transcription factor (TF) families are conserved, the C2H2 zinc finger (ZNF) family stands out as a notable exception. In particular, novel ZNF gene types have arisen, duplicated, and diverged independently throughout evolution to yield many lineage-specific TF genes. This evolutionary dynamic not only raises many intriguing questions but also severely complicates identification of those ZNF genes that remain functionally conserved. To address this problem, we searched for vertebrate “DNA binding orthologs” by mining ZNF loci from eight sequenced genomes and then aligning the patterns of DNA-binding amino acids, or “fingerprints,” extracted from the encoded ZNF motifs. Using this approach, we found hundreds of lineage-specific genes in each species and also hundreds of orthologous groups. Most groups of orthologs displayed some degree of fingerprint divergence between species, but 174 groups showed fingerprint patterns that have been very rigidly conserved. Focusing on the dynamic KRAB-ZNF subfamily—including nearly 400 human genes thought to possess potent KRAB-mediated epigenetic silencing activities—we found only three genes conserved between mammals and nonmammalian groups. These three genes, members of an ancient familial cluster, encode an unusual KRAB domain that functions as a transcriptional activator. Evolutionary analysis confirms the ancient provenance of this activating KRAB and reveals the independent expansion of KRAB-ZNFs in every vertebrate lineage. Most human ZNF genes, from the most deeply conserved to the primate-specific genes, are highly expressed in immune and reproductive tissues, indicating that they have been enlisted to regulate evolutionarily divergent biological traits.

KRAB zinc finger proteins

“…Third, KAP1 deletion in neuronal progenitors activates some endogenous retroelements (Fasching et al, 2015), and selected ERVs are similarly induced in murine B lymphocytes or mouse embryonic fibroblasts (MEFs) depleted for SETDB1 (Collins et al, 2015;Wolf et al, 2015b). Correspondingly, human KRAB-ZFPs display extensive and cell-specific patterns of expression in all adult tissues examined Liu et al, 2014). Furthermore, the mouse-specific KRAB-ZFPs ZFP932 and Gm15446 are also involved in controlling their TE targets in somatic tissues, where they modulate the TE-mediated regulation of neighboring genes in vivo (Ecco et al, 2016).…”

“…Studies in human and mouse showed that KAP1 depletion in these cells leads to differentiation and metabolic defects (Santoni de Sio et al, 2012a,,b;Chikuma et al, 2012). The KRAB-ZFPs responsible for these phenotypes, however, have not yet been identified, but many are specifically expressed in these tissues (Liu et al, 2014;Imbeault et al, 2017). Other events influenced by KRAB-ZFPs include osteogenesis (Jheon et al, 2001), mammary gland development (Oliver et al, 2012) and the formation of extra-embryonic tissues .…”

“…the series of amino acid triplets within their ZNF arrays predicted to dictate their DNA-binding specificity) have been compared (Liu et al, 2014;Imbeault et al, 2017). These analyses delineated clusters that are specific for most taxonomic orders and also allowed for the identification of KRAB-ZFPs restricted to each species .…”

“…During evolution, KRAB-ZFP genes underwent strong positive selection at positions encoding amino acids predicted to determine the DNAbinding specificity of their products (Emerson and Thomas, 2009;Liu et al, 2014). Furthermore, KRAB-ZFP paralogs exhibit not only significant differences in ZNF fingerprints, but also differential expression and splicing patterns across tissues, consistent with the acquisition of new functions following gene duplication events (Nowick et al, 2010;Kauzlaric et al, 2017).…”

“…KRAB-ZFP genes first emerged more than 400 million years ago, and are now encoded in the hundreds by all modern tetrapods examined to date, with the notable exception of birds, in which they generally do not exceed ten (Emerson and Thomas, 2009;Liu et al, 2014;Imbeault et al, 2017;Kauzlaric et al, 2017). KRAB-ZFPs are characterized by an N-terminal Krüppel-associated box (KRAB) domain and a C-terminal array of C 2 H 2 zinc fingers (ZNFs) (Urrutia, 2003).…”