KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

Abstract

The human genome encodes some 350 Krüppel-associated box (KRAB) domain-containing zinc-finger proteins (KZFPs), the products of a rapidly evolving gene family that has been traced back to early tetrapods. The function of most KZFPs is unknown, but a few have been demonstrated to repress transposable elements in embryonic stem (ES) cells by recruiting the transcriptional regulator TRIM28 and associated mediators of histone H3 Lys9 trimethylation (H3K9me3)-dependent heterochromatin formation and DNA methylation. Depletion of TRIM28 in human or mouse ES cells triggers the upregulation of a broad range of transposable elements, and recent data based on a few specific examples have pointed to an arms race between hosts and transposable elements as an important driver of KZFP gene selection. Here, to obtain a global view of this phenomenon, we combined phylogenetic and genomic studies to investigate the evolutionary emergence of KZFP genes in vertebrates and to identify their targets in the human genome. First, we unexpectedly reassigned the root of the family to a common ancestor of coelacanths and tetrapods. Second, although we confirmed that the majority of KZFPs bind transposable elements and pinpoint cases of ongoing co-evolution, we found that most of their transposable element targets have lost all transposition potential. Third, by examining the interplay between human KZFPs and other transcriptional modulators, we obtained evidence that KZFPs exploit evolutionarily conserved fragments of transposable elements as regulatory platforms long after the arms race against these genetic invaders has ended. Together, our results demonstrate that KZFPs partner with transposable elements to build a largely species-restricted layer of epigenetic regulation.

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.…”

“…It was then suspected that the primary role of KRAB-ZFPs was to silence TEs, and that their evolutionary selection represented the host component of an arms race against these genetic invaders (Jacobs et al, 2014;Castro-Diaz et al, 2014;Thomas and Schneider, 2011). More recent data, however, suggest that KRAB-ZFPs fulfill a role that is far more elaborate and, in some cases at least, can contribute to the domestication of their TE targets for the benefit of the host (Ecco et al, 2016;Imbeault et al, 2017).…”

“…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.…”

“…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).…”