DNA methylation plays an important role in promoter choice and protein production at the mouse Dnmt3L locus

The DNA methyltransferase 3-like (Dnmt3L) protein is a crucial cofactor in the germ line for the de novo methyltransferase Dnmt3a, which establishes imprints and represses transposable elements. We have previously shown that Dnmt3L transcription is regulated via three different promoters in mice, producing transcripts we term Dnmt3Ls (stem cell), Dnmt3Lo (oocyte) and Dnmt3Lat (adult testis). Here we show that both Dnmt3Ls and Dnmt3Lo produce full-length proteins but that the Dnmt3Lat transcripts are not translated. Although not a canonical CpG island, the Dnmt3Ls promoter is silenced by methylation during somatic differentiation in parallel with germ-cell-specific genes. During oocyte growth, Dnmt3Ls also becomes heavily methylated and silenced and this requires its own gene product, since there is complete loss of methylation and derepression of transcription from this promoter in oocytes derived from Dnmt3L−/− mice. Methylation of the Dnmt3Ls promoter is established prior to the completion of imprinting and explains the requirement in mouse oocytes for the Dnmt3Lo promoter, located in an intron of the neighboring unmethylated Aire gene. Overall these results give insight into how and why promoter switching at the mouse Dnmt3L locus occurs and provide one of the first examples of a non-imprinted locus where methylation plays a role in promoter choice. The derepression of the Dnmt3Ls promoter in the knockout oocytes also suggests that other non-imprinted loci may be dysregulated in these cells and contribute to the phenotype of the resultant mice.

► The Dnmt3L protein is required for DNA methylation in germ cells. ► Dnmt3L has three promoters, active in stem cells (Dnmt3Ls), adult testis (Dnmt3Lat) or oocytes (Dnmt3Lo). ► While Dnmt3Lo and Dnmt3Ls both produce protein, switching to Dnmt3Lat shuts down protein production in adult testis. ► The Dnmt3Ls promoter is itself methylated in oocytes, but methylation and repression are lost in Dnmt3L−/− ovaries. ► Dnmt3Ls is shut down prior to completion of imprinting in oocytes, explaining the requirement for Dnmt3Lo in these cells.