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

The human genome encodes some 350 Kruppel-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(1,2). 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(3-9). Depletion of TRIM28 in human or mouse ES cells triggers the upregulation of a broad range of transposable elements(4,10,11), 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(5). 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.

Transposable Elements, Polydactyl Proteins, and the Genesis of Human-Specific Transcription Networks

Didier Trono

Transposable elements (TEs) may account for up to two-thirds of the human genome, and as genomic threats they are subjected to epigenetic control mechanisms engaged from the earliest stages of embryonic development. We previously determined that an important component of this process is the sequence-specific recognition of TEs by KRAB (Krüppel-associated box)-containing zinc-finger proteins (KRAB-ZFPs), a large family of tetrapod-restricted transcription factors that act by recruiting inducers of heterochromatin formation and DNA methylation. We further showed that KRAB-ZFPs and their cofactor KAP1 exert a marked influence on the transcription dynamics of embryonic stem cells via their docking of repressor complexes at TE-contained regulatory sequences. It is generally held that, beyond this early embryonic period, TEs become permanently silenced, and that the evolutionary selection of KRAB-ZFPs and other TE controllers is the result of a simple evolutionary arms race between the host and these genetics invaders. Here, I discuss recent evidence that invalidates this dual assumption and instead suggests that KRAB-ZFPs are the instruments of a massive enterprise of TE domestication, whereby transposon-based regulatory sequences and their cellular ligands establish species-specific transcription regulation networks that influence multiple aspects of human development and physiology.

2016

Transposable elements and their KRAB/KAP1 controllers broadly regulate transcription in adult human cells

Flavia Marzetta

KAP1 is a universal corepressor for the large family of KRAB-ZFP proteins that coordinates epigenetic silencing of endogenous retroelements (EREs) during early embryonic development. This process is essential not just to prevent replication of EREs, but also to control their regulatory influence on host genes. Although in differentiated cells the control of EREs is believed to be mainly DNA methylation-dependent, emerging evidence suggests that KAP1-dependent, histone-based repression might remain a key regulator of ERE expression and its influence on cellular gene networks. Using a combination of transcriptional and histone modification profiling, we have investigated the impact of KAP1 epigenetic regulation on the transcriptional dynamics of human CD4+ T cells. We found that KAP1 binding on subsets of EREs is maintained in differentiated CD4+ T cells, where its locus-specific recruitment is dynamically modulated along with the T cell activation status. KAP1 depletion by RNA interference leads to a global decrease in repressive histone modifications that is accompanied by broad transcriptional alterations. Indeed, not only a large fraction of EREs become derepressed, but their deregulation correlates with illegittimate activation of nearby genes. Correspondingly, loss of KAP1 unleashes the intrinsic regulatory activities that some EREs are endowed with, suggesting a functional link between control of mobile genetic elements and protection of lineage-specific transcriptional networks. These findings establish the KRAB/KAP1 system as an important safeguard of CD4+ T cells transcriptional identity and suggest a critical role in maintaining epigenetic silencing of ERE-based regulatory sequences in adult tissues. Furthermore, our study shed light onto a previously unappreciated contribution of retrotransposon-derived sequences to the complexity of the human T cell transcriptome. A better knowledge of the physiological transcriptional activity of these mobile genetic elements, as well as their control mechanisms throughout development, would greatly help the debate on their pathologic implications.

EPFL2015

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.