rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline

Abstract

Transcriptional silencing by heritable cytosine-5 methylation is an ancient strategy to repress transposable elements. It was previously thought that mammals possess four DNA methyltransferase paralogs—Dnmt1, Dnmt3a, Dnmt3b and Dnmt3l—that establish and maintain cytosine-5 methylation. Here we identify a fifth paralog, Dnmt3c, that is essential for retrotransposon methylation and repression in the mouse male germline. From a phenotype-based forward genetics screen, we isolated a mutant mouse called ‘rahu’, which displays severe defects in double-strand-break repair and homologous chromosome synapsis during male meiosis, resulting in sterility. rahu is an allele of a transcription unit (Gm14490, renamed Dnmt3c) that was previously mis-annotated as a Dnmt3-family pseudogene. Dnmt3c encodes a cytosine methyltransferase homolog, and Dnmt3crahu mutants harbor a non-synonymous mutation of a conserved residue within one of its cytosine methyltransferase motifs, similar to a mutation in human DNMT3B observed in patients with immunodeficiency, centromeric instability and facial anomalies syndrome. The rahu mutation lies at a potential dimerization interface and near the potential DNA binding interface, suggesting that it compromises protein-protein and/or protein-DNA interactions required for normal DNMT3C function. Dnmt3crahu mutant males fail to establish normal methylation within LINE and LTR retrotransposon sequences in the germline and accumulate higher levels of transposon-derived transcripts and proteins, particularly from distinct L1 and ERVK retrotransposon families. Phylogenetic analysis indicates that Dnmt3c arose during rodent evolution by tandem duplication of Dnmt3b, after the divergence of the Dipodoidea and Muroidea superfamilies. These findings provide insight into the evolutionary dynamics and functional specialization of the transposon suppression machinery critical for mammalian sexual reproduction and epigenetic regulation.

MiR‐199‐3p–Dnmt3a–STAT3 signalling pathway in ovalbumin‐induced allergic rhinitis

“…Dnmt3l lacks a catalytic domain, but can assist Dnmt3a and Dnmt3b. It is responsible for methylating the promoter regions of recently evolved retrotransposons in the male germline and suppresses the expression of those 'young and dangerous' transposons during early spermatogenesis, and thus is necessary for mouse fertility (Barau et al, 2016;Jain et al, 2017). Dnmt3c is a newly identified de novo methyltransferase, which seems to have arisen from a duplication event of Dnmt3b in the rodent genome, and was first annotated as a pseudogene.…”

“…There are mainly three types of DNA methyltransferases in mammals, Dnmt1 (Svedruzic, 2008), Dnmt3a (Yang, Rau, & Goodell, 2015) and Dnmt3b (Duan et al, 2015). The Dnmt3 family consists of Dnmt3a, Dnmt3b, Dnmt3l and Dnmt3c (Barau et al, 2016;Jain et al, 2017), the last of which was recently discovered only in the rodent genome. Dnmt3a and Dnmt3b are well known for generating a de novo methylation pattern (Chedin, 2011).…”

“…Dnmt3c is a newly identified de novo methyltransferase, which seems to have arisen from a duplication event of Dnmt3b in the rodent genome, and was first annotated as a pseudogene. It is responsible for methylating the promoter regions of recently evolved retrotransposons in the male germline and suppresses the expression of those 'young and dangerous' transposons during early spermatogenesis, and thus is necessary for mouse fertility (Barau et al, 2016;Jain et al, 2017). Dnmt1 is the key maintenance methyltransferase, which has much higher enzyme activity in methylating CpGs on hemimethylated DNAs than on unmethylated ones (Hermann, Goyal, & Jeltsch, 2004).…”

Dynamic evolution of de novo DNA methyltransferases in rodent and primate genomes

“…Closer phylogenetic analyses in several taxa have revealed mammalian lineage-specific duplications, including the duplication and co-retention of several Dnmt1 paralogs in marsupials (17) and the evolution of Dnmt3L from Dnmt3A in eutherian mammals (18). Another gene duplication from Dnmt3B gave rise to Dnmt3C in muroid rodents where it has acquired a distinct, non-redundant role in retrotransposon repression during spermatogenesis (19, 20). Thus, a series of ancient and recent gene duplications have led to the current repertoires of mammalian DNMTs.…”

“…Two recent studies showed that DNMT3C is the crucial enzyme for this process (19, 20). Dnmt3C knock-out (KO) males are sterile and their germ cell methylation profiles are similar to those of piRNA mutants, with a 1% drop in genome-wide DNA methylation content that selectively affects the promoters of young copies of LINE and ERVK retrotransposons (20, 23, 25).…”