Endogenous Retroviral Sequences Behave as Putative Enhancers Controlling Gene Expression through HP1-Regulated Long-Range Chromatin Interactions

Cells. 2022 Aug 3;11(15):2392. doi: 10.3390/cells11152392.

Abstract

About half of the mammalian genome is constituted of repeated elements, among which endogenous retroviruses (ERVs) are known to influence gene expression and cancer development. The HP1 (Heterochromatin Protein 1) proteins are known to be essential for heterochromatin establishment and function and its loss in hepatocytes leads to the reactivation of specific ERVs and to liver tumorigenesis. Here, by studying two ERVs located upstream of genes upregulated upon loss of HP1, Mbd1 and Trim24, we show that these HP1-dependent ERVs behave as either alternative promoters or as putative enhancers forming a loop with promoters of endogenous genes depending on the genomic context and HP1 expression level. These ERVs are characterised by a specific HP1-independent enrichment in heterochromatin-associated marks H3K9me3 and H4K20me3 as well as in the enhancer-specific mark H3K4me1, a combination that might represent a bookmark of putative ERV-derived enhancers. These ERVs are further enriched in a HP1-dependent manner in H3K27me3, suggesting a critical role of this mark together with HP1 in the silencing of the ERVs, as well as for the repression of the associated genes. Altogether, these results lead to the identification of a new regulatory hub involving the HP1-dependent formation of a physical loop between specific ERVs and endogenous genes.

Keywords: HP1; Trim24; chromatin organization; endogenous retroviruses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / genetics
  • Chromobox Protein Homolog 5
  • Endogenous Retroviruses* / genetics
  • Gene Expression
  • Heterochromatin
  • Mammals / genetics

Substances

  • Chromatin
  • Heterochromatin
  • Chromobox Protein Homolog 5

Grants and funding

This research was funded by the Agence Nationale de la Recherche (CHRODYT, ANR-16-CE15-0018-04 to F.C. and T.F.), the AFM-Téléthon (N°21024 to T.F.), the Centre National de la Recherche Scientifique and the Institut National de la Santé et de la Recherche Médicale.