Roles of endogenous retroviruses in transcriptional condensates

Abstract

Endogenous retroviruses (ERVs) are repetitive elements that constitute around 10 percent of mammalian genomes. ERVs need to be kept transcriptionally silenced during development and ERV upregulation is linked to loss of pluripotency and mouse embryonic lethality. Precise mechanistic understanding of this process remains incomplete. To investigate effects of ERV derepression, I utilized degradation tag (dTAG) system to acutely deplete endogenous levels of TRIM28, a heterochromatin protein that recruits silencing machinery to ERVs in mouse embryonic stem cells (mESCs). Nascent transcriptome sequencing indicated TRIM28 depletion induces acute transcriptomic changes: upregulation of ERVs and other targets of TRIM28-mediated repression and simultaneous downregulation of key pluripotency super enhancers (SEs) and associated genes. High-resolution microscopy data indicated ERV derepression reduces association of SEs with RNA polymerase II (RNAPII) and Mediator (MED1), the key components of transcriptional condensates. In turn, derepressed ERVs associated with RNAPII and MED1, indicating transcriptional condensate components are redistributed upon TRIM28 depletion. Presence of transcriptional machinery at derepressed ERV loci upregulated nearby genes, including Cthrc1. Ectopic overexpression of pluripotency factors enriched at SEs prevented the reduction in transcriptional condensate association with SEs. ERV knockdown rescued transcriptional condensate localization indicating RNAs produced at ERV play an important in transcriptional condensate redistribution. Evidence presented here shows derepressed ERVs have the capacity to ‘hijack’ transcriptional condensates from key pluripotency genes upon TRIM28 degradation. This may be the molecular mechanism contributing to embryonic lethality associated with ERV derepression in TRIM28 knockout mice.