Abstract
Retrotransposition of endogenous retroviruses (ERVs) poses a substantial threat to genome stability. Transcriptional silencing of a subset of these parasitic elements in early mouse embryonic and germ cell development is dependent upon the lysine methyltransferase SETDB1, which deposits H3K9 trimethylation (H3K9me3) and the co-repressor KAP1, which binds SETDB1 when SUMOylated. Here we identified the transcription co-factor hnRNP K as a novel binding partner of the SETDB1/KAP1 complex in mouse embryonic stem cells (mESCs) and show that hnRNP K is required for ERV silencing. RNAi-mediated knockdown of hnRNP K led to depletion of H3K9me3 at ERVs, concomitant with de-repression of proviral reporter constructs and specific ERV subfamilies, as well as a cohort of germline-specific genes directly targeted by SETDB1. While hnRNP K recruitment to ERVs is dependent upon KAP1, SETDB1 binding at these elements requires hnRNP K. Furthermore, an intact SUMO conjugation pathway is necessary for SETDB1 recruitment to proviral chromatin and depletion of hnRNP K resulted in reduced SUMOylation at ERVs. Taken together, these findings reveal a novel regulatory hierarchy governing SETDB1 recruitment and in turn, transcriptional silencing in mESCs.
Highlights
Long terminal repeat (LTR) retrotransposons, called endogenous retroviruses (ERVs), are the relics of ancient and more recent germline retroviral integrations, comprising ~8–10% of the mouse and human genomes, respectively [1]
SETDB1 is recruited to ERVs by its binding partner KAP1, the molecular basis of this silencing pathway is not clear
Using biochemical and genetic approaches, we identified heterogeneous nuclear ribonucleoprotein K (hnRNP K) as a novel component of this silencing pathway that facilitates the recruitment of SETDB1 to ERVs to promote their repression
Summary
Long terminal repeat (LTR) retrotransposons, called endogenous retroviruses (ERVs), are the relics of ancient and more recent germline retroviral integrations, comprising ~8–10% of the mouse and human genomes, respectively [1]. DNA methylation suppresses ERV transcription in differentiated somatic cells [5], pluripotent stem cell lines derived from the inner cell mass of the blastocyst, such as murine embryonic stem cells (mESCs) utilize a DNA methylation-independent pathway to maintain ERV silencing [6]. Key effectors in this silencing pathway are the conserved Krüppelassociated box zinc finger proteins (KRAB-ZFPs), the largest family of C2H2 zinc finger transcription factors in vertebrate genomes [7]. KAP1 is apparently recruited to IAP elements via sequences in the 5’UTR downstream of the PBS [14]
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