Epigenetic repression of intronless mobile elements by the HUSH complex

Abstract

The mammalian genome is under constant threat from invasion by mobile genetic elements including transposons and viruses. To defend the genome, cells recognize incoming DNA and limit its transcription through repressive chromatin modifications. The human silencing hub (HUSH) complex transcriptionally represses long interspersed element-1 retrotransposons (L1s) and retroviruses through histone H3 Lys9 trimethylation (H3K9me3). How HUSH recognizes and initiates silencing of these invading genetic elements is unknown. By monitoring transcription from L1 transgenes, I found that incoming L1s are recognized by HUSH independently of their integration sites, a critical difference with previously studied viral silencing. By studying sequence determinants of L1 repression by HUSH, I discovered that HUSH is able to recognize and transcriptionally repress a broad range of sequence-diverse, intronless invading DNAs, despite no prior exposure to such DNAs. Sequence length and high adenine (A) content in the sense strand are important additional determinants of susceptibility to HUSH-targeting. My further work demonstrated that Periphilin binds transcripts from the target locus, prior to and independent of, H3K9me3 deposition, which explains why target transcription is essential for both initiation and propagation of HUSH-mediated H3K9me3. Whilst diverse intronless transgenes are susceptible to HUSH-repression, I found that the presence of an intron counteracts repression, even in the absence of intron splicing. A subset of endogenous intronless loci are silenced by HUSH, and Periphilin specifically binds transcripts from endogenous intronless loci. Therefore, intronless DNA, the product of reverse transcription, provides a versatile means to distinguish invading RNA-derived retroelements from intron-containing host genes and provides a mechanism by which HUSH protects the genome from ‘non-self’ DNA. I propose that HUSH is a component of the innate immune system and intronless DNA the molecular pattern recognized by HUSH. By silencing cDNA, the product of reverse transcription, HUSH controls the reverse flow of genetic information (i.e. from RNA to DNA) in the human genome.