Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons

In the first days of embryogenesis, transposable element-embedded regulatory sequences (TEeRS) are silenced by Kruppel-associated box (KRAB) zinc finger proteins (KZFPs). Many TEeRS are subsequently co-opted in transcription networks, but how KZFPs influence this process is largely unknown. We identify ZNF417 and ZNF587 as primate-specific KZFPs repressing HERVK (human endogenous retrovirus K) and SVA (SINE-VNTR-Alu) integrants in human embryonic stem cells (ESCs). Expressed in specific regions of the human developing and adult brain, ZNF417/587 keep controlling TEeRS in ESC-derived neurons and brain organoids, secondarily influencing the differentiation and neurotransmission profile of neurons and preventing the induction of neurotoxic retroviral proteins and an interferon-like response. Thus, evolutionarily recent KZFPs and their TE targets partner up to influence human neuronal differentiation and physiology.

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

Pierre-Yves Joseph Laurent Helleboid, Michaël Imbeault, Didier Trono

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.

Nature Publishing Group2017

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

Global and stage specific patterns of krüppel-associated-box zinc finger protein gene expression in murine early embryonic cells

Andrea Corsinotti, Bart Deplancke, Michaël Imbeault, Adamantia Kapopoulou, Yoann Mouscaz, Helen Mary Rowe, Didier Trono

Highly coordinated transcription networks orchestrate the self-renewal of pluripotent stem cell and the earliest steps of mammalian development. KRAB-containing zinc finger proteins represent the largest group of transcription factors encoded by the genomes of higher vertebrates including mice and humans. Together with their putatively universal cofactor KAP1, they have been implicated in events as diverse as the silencing of endogenous retroelements, the maintenance of imprinting and the pluripotent self-renewal of embryonic stem cells, although the genomic targets and specific functions of individual members of this gene family remain largely undefined. Here, we first generated a list of Ensembl-annotated KRAB-containing genes encoding the mouse and human genomes. We then defined the transcription levels of these genes in murine early embryonic cells. We found that the majority of KRAB-ZFP genes are expressed in mouse pluripotent stem cells and other early progenitors. However, we also identified distinctively cell- or stage-specific patterns of expression, some of which are pluripotency-restricted. Finally, we determined that individual KRAB-ZFP genes exhibit highly distinctive modes of expression, even when grouped in genomic clusters, and that these cannot be correlated with the presence of prototypic repressive or activating chromatin marks. These results pave the way to delineating the role of specific KRAB-ZFPs in early embryogenesis.

Public Library of Science2013

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

Flavia Marzetta

EPFL2015