Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues

KRAB-containing zinc finger proteins (KRAB-ZFPs) are early embryonic controllers of transposable elements (TEs), which they repress with their cofactor KAP1 through histone and DNA methylation, a process thought to result in irreversible silencing. Using a target-centered functional screen, we matched murine TEs with their cognate KRAB-ZFP. We found the paralogs ZFP932 and Gm15446 to bind overlapping but distinguishable subsets of ERVK (endogenous retrovirus K), repress these elements in embryonic stem cells, and regulate secondarily the expression of neighboring genes. Most importantly, 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. Therefore, TEs and KRAB-ZFPs establish transcriptional networks that likely regulate not only development but also many physiological events. Given the high degree of species specificity of TEs and KRAB-ZFPs, these results have important implications for understanding the biology of higher vertebrates, including humans.

KRAB'n'KAP, DNA methylation and epigenetic memory

Andrea Coluccio

The KZFP/KAP1 (Krüppel associated box zinc finger proteins/KRAB-associated protein 1) complex is a transcriptional repressor that triggers the deposition of heterochromatin (H3K9me3) and DNA methylation. The main targets of the KZFP/KAP1 complex are transposable elements (TEs), which are generally maintained transcriptionally inactive to avoid retrotransposition and preserve genomic stability, and imprinting control regions (ICRs), where DNA methylation is protected to ensure proper parent-of-origin specific expression of crucial developmental genes. The role of the KZFP/KAP1 system in forming a heterochromatic environment is of particular relevance during the wave of genome-wide epigenetic reprogramming that takes place in the early embryo between fertilization and implantation. During these stages, TEs and ICRs are amongst the few sequences that retain the epigenetic information inherited from the gametes. While the importance of KZFP/KAP1 in maintenance of imprinting and TE silencing is well established, the mechanisms by which KAP1 counteracts demethylation and interacts with this epigenetically unstable environment to regulate TEs are still largely unknown. In this work, we uncover the complex interplay between KAP1, DNA methylation and active demethylation in maintaining imprinting and regulating TE expression in naïve embryonic stem cells. We first confirmed that KAP1 was able to bind and repress TEs in absence of DNA methylation. We then demonstrated that the KZFP/KAP1 complex was required to maintain heterochromatin and DNA methylation at ICRs and TEs, and was able to protect these sequences from active demethylation. We comprehensively characterized the responsiveness of TEs to removal of KAP1 in absence of DNA methylation and active demethylation, which unveiled a complex, multi-layered and integrant-specific regulation for these elements. ZFP57 is known to recruit KAP1 on ICRs, but here we identified ZNF445 as a second KZFP that specifically binds ICRs both in human and mouse. We found that ZNF445 regulates imprinting differentially in human versus murine embryonic stem cells. Our findings suggest for the first time that two different KZFPs could have evolved with species-specific roles in imprinting regulation. The high degree of conservation of ZNF445 in the human population argues in favour of a previously unsuspected critical role for this protein in development. This work provides useful insights in the role of KAP1 and its KZFPs partners both in preserving epigenetic memory and in transposon silencing during early development.

EPFL2017

Evolutionally dynamic control of LINE-1 elements in embryonic stem cells

Natali Pennese

Mobile elements are important evolutionary forces that challenge genomic integrity. Long interspersed element-1 (L1, also known as LINE-1) is the only autonomous transposon still active in the human genome. It displays an unusual pattern of evolution, with at any given time a single active L1 lineage amplifying to thousands of copies before getting replaced by a new lineage likely under pressure of host restriction factors, which act notably by silencing L1 expression during early embryogenesis. Here, we demonstrate that in human embryonic stem cells (hESC) KAP1, the master co-factor of KRAB-containing zinc finger proteins (KRAB-ZFP) previously implicated in the restriction of endogenous retroviruses, represses a discrete subset of L1 lineages predicted to have entered the ancestral genome between 26.8 and 7.6 million years ago. In the mouse, we documented a similar chronologically conditioned pattern, albeit with a much contracted time scale. We could further identify an L1-binding KRAB-ZFP, suggesting that this rapidly evolving protein family is more globally responsible for L1 recognition. KAP1 knockdown in hESC induced the expression of KAP1-bound L1 elements, but their younger, human-specific counterparts (L1Hs) were unaffected. Instead, they were stimulated by depleting DNA methyltransferases, consistent with recent evidence demonstrating that the PIWI-piRNA pathway regulates L1Hs in hESC. Altogether, these data indicate that the early embryonic control of L1 is an evolutionary dynamic process, and support a model whereby newly emerged lineages are first suppressed by DNA methylation-inducing small RNA-based mechanisms, before KAP1-recruiting protein repressors are selected.

EPFL2015

KRAB'n'KAP, DNA methylation and epigenetic memory

Andrea Coluccio

EPFL2017