De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET

Endogenous retroviruses (ERVs) undergo de novo DNA methylation during the first few days of mammalian embryogenesis, although the factors that control the targeting of this process are largely unknown. We asked whether KAP1 (KRAB-associated protein 1) is involved in this mechanism because of its previously defined role in maintaining the silencing of ERVs through the histone methyltransferase ESET and histone H3 lysine 9 trimethylation. Here, we demonstrate that introduced ERV sequences are sufficient to direct rapid de novo methylation of a flanked promoter in embryonic stem (ES) cells. This mechanism requires the presence of an ERV sequence-recognizing KRAB zinc-finger protein (ZFP) and both KAP1 and ESET. Furthermore, this process can also take place on a strong cellular promoter and leads to methylation signatures that are subsequently maintained in vivo throughout embryogenesis. Finally, we show that methylation of ERVs residing in the genome is affected by knockout of KAP1 in early embryos. KRAB-ZFPs, KAP1 and ESET are thus likely to be responsible for the early embryonic instatement of stable epigenetic marks at ERV-containing loci.

Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements

Julien Léonard Duc, Adamantia Kapopoulou, Flavia Marzetta, Charlène Mireille Raymonde Raclot, Didier Trono, Priscilla Turelli

Reverse transcription-derived sequences account for at least half of the human genome. Although these retroelements are formidable motors of evolution, they can occasionally cause disease, and accordingly are inactivated during early embryogenesis through epigenetic mechanisms. In the mouse, at least for endogenous retroviruses, important mediators of this process are the tetrapod-specific KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor TRIM28. The present study demonstrates that KRAB/TRIM28-mediated regulation is responsible for controlling a very broad range of human-specific endogenous retroelements (EREs) in human embryonic stem (ES) cells and that it exerts, as a consequence, a marked effect on the transcriptional dynamics of these cells. It further reveals reciprocal dependence between TRIM28 recruitment at specific families of EREs and DNA methylation. It finally points to the importance of persistent TRIM28-mediated control of ERE transcriptional impact beyond their presumed inactivation by DNA methylation.

Cold Spring Harbor Lab Press, Publications Dept2014

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

KRAB'n'KAP, DNA methylation and epigenetic memory

Andrea Coluccio

EPFL2017