Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites

Abstract

Long interspersed elements (LINEs), through both self-mobilization and trans-mobilization of short interspersed elements and processed pseudogenes, have made an indelible impact on the structure and function of the human genome. One consequence is the creation of new CpG islands (CGIs). In fact, more than half of all CGIs in the genome are associated with repetitive DNA, three-quarters of which are derived from retrotransposons. However, little is known about the epigenetic impact of newly inserted CGIs. We utilized a transgenic LINE-1 mouse model and tracked DNA methylation dynamics of individual germline insertions during mouse development. The retrotransposed GFP marker sequence, a strong CGI, is hypomethylated in male germ cells but hypermethylated in somatic tissues, regardless of genomic location. The GFP marker is similarly methylated when delivered into the genome via the Sleeping Beauty DNA transposon, suggesting that the observed methylation pattern may be independent of the mode of insertion. Comparative analyses between insertion-and noninsertion-containing alleles further reveal a graded influence of the retrotransposed CGI on flanking CpG sites, a phenomenon that we described as "sloping shores." Computational analyses of human and mouse methylomic data at single-base resolution confirm that sloping shores are universal for hypomethylated CGIs in sperm and somatic tissues. Additionally, the slope of a hypomethylated CGI can be affected by closely positioned CGI neighbors. Finally, by tracing sloping shore dynamics through embryonic and germ cell reprogramming, we found evidence of bookmarking, a mechanism that likely determines which CGIs will be eventually hyper-or hypomethylated.

Intact piRNA pathway prevents L1 mobilization in male meiosis

“…A recent analysis of the Dnmt3l mutant suggests that the loss of DNA methylation at retrotransposon sequences may alter the meiotic chromatin landscape as well as the sites of homologous recombination (22). Unmethylated retrotransposons may also change the expression profile of neighboring genes that are important for meiotic functions, as they can reduce the methylation level at surrounding sites through the formation of sloping shores (45). At the protein level, overexpression of L1 ORF2 protein (ORF2p) is cytotoxic to cultured cells (60)(61)(62).…”

“…Cells were gated according to the GFP fluorescence intensity and cell granularity (see supplemental figure S2 in ref. 45). For isolating germ cells from adult animals, an optimized Hoechst 33342-based flow cytometry protocol (51) was used.…”

“…The first was from a mouse (B2346) carrying a constitutively active CAG-ORFeus transgene, which retrotransposed at ∼0.4 insertions per cell in most tissues (25). The second control was from a mouse (R605) carrying a germline insertion that had been segregated from the donor transgene (45). Both positive controls showed robust PCR signals at the expected amplicon size in the heart, liver, and testis (Fig.…”

How retrotransposons shape genome regulation

“…However, several mechanisms such as DNA and histone methylation and RNAi, actively suppress retrotransposon expression. The epigenetic mechanisms controlling retroelements may well follow retrotransposons during their movement “around” the genome and thereby modify the epigenetic control of retrotransposition targeted loci [59,60]. Below we describe ways of retrotransposon repression that contributed to sculpt the modern genome and its regulatory mechanisms.…”

The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells

“…In this regard, it has been shown that most DNA methylation changes associated with development and cancer do not occur in CpG islands, but rather in sequences up to 2-kb away, which were termed CpG island shores (Doi et al 2009;Irizarry et al 2009). A recent study has shown that hypomethylated CpG islands create sloping CpG island shores (Grandi et al 2015). Interestingly, Alu elements tend to be excluded from promoter regions but are enriched in nearby regions, including CpG island shores.…”