KRAB zinc finger proteins | EPFL Graph Search

Kruppel-associated box domain zinc finger proteins (KRAB-ZFPs) are the largest family of transcriptional regulators in higher vertebrates. Characterized by an N-terminal KRAB domain and a C-terminal array of DNA-binding zinc fingers, they participate, together with their co-factor KAP1 (also known as TRIM28), in repression of sequences derived from transposable elements (TEs). Until recently, KRAB-ZFP/KAP1-mediated repression of TEs was thought to lead to irreversible silencing, and the evolutionary selection of KRAB-ZFPs was considered to be just the host component of an arms race against TEs. However, recent advances indicate that KRAB-ZFPs and their TE targets also partner up to establish species-specific regulatory networks. Here, we provide an overview of the KRAB-ZFP gene family, highlighting how its evolutionary history is linked to that of TEs, and how KRAB-ZFPs influence multiple aspects of development and physiology.

Beyond silence : a functional and evolutionary study of KRAB zinc finger proteins

Pierre-Yves Joseph Laurent Helleboid

Transposable elements (TEs) are genetic units capable of spreading within the genomes of their host. TEs contribute a readily recognizable 45% of the human DNA, reflecting in part their co-option for some as source of protein-coding sequences, for others as regulators of genome architecture and expression. Nevertheless, new TE integrants can occasionally cause diseases. The KZFP/KAP1 (KRAB-Zinc Finger Protein /KRAB-associated Protein 1) system plays a major role in the transcriptional control of TEs. Encoded in the hundreds by the genomes of most higher vertebrates, KZFPs are endowed with a N-terminal KRAB (KruÌppel- associated box) domain, some of which can recruit KAP1, and a C-terminal array of zinc fingers (ZNF) with polynucleotide binding potential. When we started this work, KZFP genes were thought to be restricted to tetrapods, and a few of their products had been found to tether KAP1 and associated heterochromatin-inducing factors to TE-derived sequences during mouse or human early embryogenesis, resulting in the deposition at these loci of H3K9me3 (histone 3 trimethylated on lysine 9) and DNA methylation, two repressive marks. Additionally, the KZFP/KAP1 system had been implicated in events as diverse as imprinting, cell differentiation and metabolic homeostasis. In order to gain insight into the biology of human KZFPs, we first performed a large-scale identification of their genomic targets. We found that the majority was enriched at TEs, where they bound to regions also recognized by other TFs. Accordingly, many KZFP-targeted TE loci displayed differential chromatin patterns in human tissues, consistent notably with their putative role of cell-specific enhancers. This strongly suggests that KZFPs participate in orchestrating TE-modulated regulatory networks. Finally, we could trace KZFP genes to a common ancestor of the coelacanth, lungfishes and tetrapods, and determined that their evolutionary emergence was most often contemporaneous to that of their TE targets, with signs supporting both an arms race and a domestication model. To pursue this exploration, we analyzed the protein partners of more than a hundred human KZFPs. We could observe that the interactome of evolutionarily recent KZFPs mainly comprised KAP1 and associated effectors, whereas that of more ancient family members, conserved from marsupials to sauropsids, tended not to associate with KAP1 and were likely to engage in interactions with more original factors, including proteins related to RNA processing or genome architecture. While these results suggested that KAP1 binding might have been a late emerging property of KZFPs, we could demonstrate that KRAB domains derived from Latimeria chalumnae associated with the cognate KAP1 protein, albeit not with its human orthologue. These results support a model whereby KZFPs first emerged as TE- controlling repressors, were continuously renewed by turnover of their hostsâ TE loads, and occasionally produced derivatives that escaped this evolutionary flushing by development and exaptation of novel functions. In sum, this work provides important insights into the evolutionary history and biological function of KRAB zinc finger proteins, the largest family of transcriptional regulators encoded by human and other higher vertebrates.

EPFL2019

Unraveling the KRAB/KAP1 control of transposable elements in pluripotent and somatic cells

Gabriela Ecco

Transposable elements (TEs) are DNA sequences able to change position in the genome, and represent more than 40% of mammalian genetic material. TEs can have positive or detrimental effects on the host, being both important motors of evolution and genomic threats, and are associated with diseases such as cancer and diabetes. Growing evidence indicates the host co-opts TEs for its benefit, with examples such as syncytins â genes important for placental formation that derive from TEs. Given their potential damaging role, the host needs to repress TEs, especially during early embryogenesis. KRAB-containing zinc finger proteins (KRAB-ZFPs) are important regulators of TEs, which they repress with their cofactor KAP1. In stem cells, the KRAB/KAP1 complex irreversibly silence TEs and is believed to be dispensable in adult cells. KRAB-ZFPs constitute one of the largest families of transcriptional regulators encoded by higher vertebrates, but functional information is missing for most of its members. To shed light on this important family of transcription factors, we first developed a large-scale functional screen matching murine TEs with their cognate KRAB-ZFP. The screen identified KRAB-ZFP809 as the ligand of its previously mapped DNA target in the murine leukemia virus genome. Our method further singled out two novel KRAB-ZFPs binding to TE sequences, as confirmed by repression and binding assays. One of them, Gm6871, was identified to regulate LINE-1 elements together with KAP1 in embryonic stem cells. KAP1 regulation followed a chronologically conditioned pattern, repressing elements that entered the mouse genome between 5.6 and 3.8 million years ago, suggestive of an evolutionary arms race between host KRAB-ZFPs and TEs. Secondly, we found the paralogs ZFP932 and Gm15446 to bind overlapping but distinguishable subsets of ERVK (endogenous retrovirus K), to repress these elements in embryonic stem cells, and to regulate secondarily the expression of neighboring genes. Furthermore, we uncovered that these KRAB-ZFPs and KAP1 control TEs in adult tissues, in cell culture and in vivo, where they partner up to modulate cellular genes. Our results establish an efficient screening method to identify KRAB-ZFPs DNA targets, opening the way to functional analyses of this major class of transcriptional repressors. Most importantly, our study strongly suggests that KRAB-ZFP genes are not only part of an evolutionary arms race with TEs, but also participate in the domestication of these elements for the benefit of the host. Given the abundance and high degree of species-specificity of TEs and KRAB-ZFPs, these results have important implications for understanding the biology of higher vertebrates, including humans.

EPFL2016

The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification

Ruedi Aebersold, Andrea Coluccio, Julien Léonard Duc, Pierre-Yves Joseph Laurent Helleboid, Michaël Imbeault, Cécile Piot, Julien Paul André Pontis, Christian Axel Wandall Thorball, Didier Trono, Priscilla Turelli

Krüppel‐associated box (KRAB)‐containing zinc finger proteins (KZFPs) are encoded in the hundreds by the genomes of higher vertebrates, and many act with the heterochromatin‐inducing KAP1 as repressors of transposable elements (TEs) during early embryogenesis. Yet, their widespread expression in adult tissues and enrichment at other genetic loci indicate additional roles. Here, we characterized the protein interactome of 101 of the ~350 human KZFPs. Consistent with their targeting of TEs, most KZFPs conserved up to placental mammals essentially recruit KAP1 and associated effectors. In contrast, a subset of more ancient KZFPs rather interacts with factors related to functions such as genome architecture or RNA processing. Nevertheless, KZFPs from coelacanth, our most distant KZFP‐encoding relative, bind the cognate KAP1. These results support a hypothetical model whereby KZFPs first emerged as TE‐controlling repressors, were continuously renewed by turnover of their hosts’ TE loads, and occasionally produced derivatives that escaped this evolutionary flushing by development and exaptation of novel functions.