Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration

Abstract

BackgroundThe ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs.ResultsHere we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny. In cancer cell lines, the newly inserted sequences typically underwent rapid transcriptional gene silencing, but they lacked cytosine methylation even after many cell divisions. L1 reporter expression was reversible and oscillated frequently. Silenced or variegated reporter expression was strongly and uniformly reactivated by treatment with inhibitors of histone deacetylation, revealing the mechanism for their silencing. By contrast, de novo integrants retrotransposed by L1 in pluripotent mouse embryonic stem (ES) cells underwent rapid silencing by dense cytosine methylation. Similarly, de novo cytosine methylation also was identified at new integrants when studied in several distinct somatic tissues of adult founder mice. Pre-existing L1 elements in cultured human cancer cells were stably silenced by dense cytosine methylation, whereas their transcription modestly increased when cytosine methylation was experimentally reduced in cells lacking DNA methyltransferases DNMT1 and DNMT3b. As a control, reporter genes mobilized by piggyBac (PB), a DNA transposon, revealed relatively stable and robust expression without apparent silencing in both cultured cancer cells and ES cells.ConclusionsWe hypothesize that the de novo methylation marks at newly inserted sequences retrotransposed by L1 in early pre-implantation development are maintained or re-established in adult somatic tissues. By contrast, histone deacetylation reversibly silences L1 reporter insertions that had mobilized at later timepoints in somatic development and differentiation, e.g., in cancer cell lines. We conclude that the cellular contexts of L1 retrotransposition can determine expression or silencing of newly integrated sequences. We propose a model whereby reporter expression from somatic TE insertions reflects the timing, molecular mechanism, epigenetic controls and the genomic, cellular and developmental contexts of their integration.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-017-0091-2) contains supplementary material, which is available to authorized users.

L1 is dynamic during neurogenesis

“…Interestingly, I found that de novo L1 remained quite hypomethylated during neural induction and neurodifferentiation. This result is consistent with previous publications that found sustained hypomethylation of de novo full-length L1 insertions from an engineered L1 reporter [222]. Therefore, I speculate that host genomes may need some rounds of cell cycling to recognize a de novo retrotransposition event and activate their defence mechanisms, in this case at the epigenetic level.…”

Long INterspersed element‐1 mobility as a sensor of environmental stresses

“…In general, the evaluation of L1–RTP through reporter gene expression causes an underestimation of L1 retrotransposition events, because the reporter cassettes integrated in epigenetically silent insertional site cannot be detected (Garcia‐Perez et al ., ; Kannan et al ., ; Macia et al ., ) and multiple retrotransposition events in a single transfected cell cannot be discriminated as well (Wei et al ., ). To gain further information, evaluation of the number of inserted engineered L1, regardless of their expression, can be carried out by quantitative real‐time PCR assays, in addition to the measurement of the reporter gene expression (Del Re et al ., ).…”

Heritable L1 Retrotransposition Events During Development: Understanding Their Origins

“…As the retrotransposition capacity of a donor L1 depends on its epigenetic regulation in a particular cell, in addition to the enzymatic efficiency of its encoded proteins, it will be interesting to determine whether de novo daughter insertions in vivo are subjected to the same epigenetic and host factor regulation as pre‐existing genomic elements, or whether there is some delay in establishing epigenetic marks upon newly‐integrated L1 copies. Recent studies employing engineered L1 elements in mouse embryonic stem cells and transgenic mice suggest the former scenario is more likely …”