DNA methylation links lagging strand replication to transposable element control

DNA methylation is an essential epigenetic mark that silences transposable elements (TEs) in mammalian genomes ^1,2 . Following DNA replication, methylation patterns must be faithfully restored ^3,4 , yet how the two processes are coordinated remains unclear. Here, using strand-specific, genome-wide analyses ^5–7 in mouse embryonic stem cells, we show that DNA methylation maintenance is coupled to the lagging-strand synthesis in TE-rich regions. Paradoxically, despite this targeting, the lagging strand is more permissive for TE integration than the leading strand. Notably, insertions of full-length LINE-1s, SINEs, and satellite repeats are all enriched on the lagging strand over evolutionary time. Consequently, most TEs, particularly young elements, are oriented head-on relative to replication forks in the mouse genome, creating an unfavorable genomic configuration ⁸ that is preferentially targeted by DNA methylation maintenance. Mechanistically, DNA methylation maintenance is coupled to the lagging-strand replication via UHRF1-LIG1 ⁹ and PCNA–PAF15 ¹⁰ interactions, and the interference in this mechanism slows Okazaki fragment maturation, and thereby potentially may facilitate TE retention. Together, we show a mechanism of TE control during DNA replication with an unexpected evolutionary interplay in which DNA methylation may facilitate, rather than solely prevent, TE expansion.