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

Devanshi Jain,Corentin Claeys Bouuaert,Cem Meydan,Kathryn V Anderson,Julian Lange,Scott Keeney,Nathalie Lailler,Christopher E Mason,Paula E Cohen

doi:10.1371/journal.pgen.1006964

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.

Highlights

Transposable elements have been described as ‘dark energy’ that acts both as a creative force, by giving rise to new genes and regulatory elements, and as a threat, by disrupting genome architecture [1]
We have generated a mutant mouse, called ‘rahu’, that fails to methylate transposons in germ cells, suffers an increase in transposon expression and is sterile. rahu mice carry a mutation in a new gene, Dnmt3c, which appeared during rodent evolution through gene duplication 45–55 million years ago and is an essential component of the germline defense system against transposons in male mice
We propose that Dnmt3c encodes a de novo DNA methyltransferase that diversified from DNMT3B during evolution of the Muroidea and that became functionally specialized for germline defense against retrotransposon activity

Summary

Introduction

Transposable elements have been described as ‘dark energy’ that acts both as a creative force, by giving rise to new genes and regulatory elements, and as a threat, by disrupting genome architecture [1]. Genomes have co-evolved with their retrotransposons and have multiple defense mechanisms to restrain transposon activity [4]. This restraint is of utmost importance in the germline, where retrotransposon activity facilitates vertical transmission, and threatens genome integrity and germ cell viability. In the mouse male germline, after a developmentally programmed methyl-cytosine erasure, retrotransposon methylation is re-established in prospermatogonia prior to birth [6,7,8,9]. Spermatogenesis initiates and spermatogonia enter a meiotic cell cycle, which encompasses an extended prophase. The spermatocyte genome experiences developmentally programmed DNA double-strand breaks (DSBs) that are subsequently repaired by homologous recombination. Failure to methylate retrotransposons leads to abnormal retrotransposon expression, spermatogenic arrest in meiotic prophase, and sterility [11, 12]

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