Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K. & Hannon, G. J. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316, 744–747 (2007).
Carmell, M. A. et al. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell 12, 503–514 (2007).
Kuramochi-Miyagawa, S. et al. DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev. 22, 908–917 (2008).
Dias Mirandela, M. et al. Two-factor authentication underpins the precision of the piRNA pathway. Nature 634, 979–985 (2024).
De Fazio, S. et al. The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements. Nature 480, 259–263 (2011).
Schopp, T. et al. TEX15 is an essential executor of MIWI2-directed transposon DNA methylation and silencing. Nat. Commun. 11, 3739 (2020).
Krull, S. et al. Protein Tpr is required for establishing nuclear pore-associated zones of heterochromatin exclusion. EMBO J. 29, 1659–1673 (2010).
Walsh, C. P., Chaillet, J. R. & Bestor, T. H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20, 116–117 (1998).
Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease. Nat. Rev. Mol. Cell Biol. 20, 590–607 (2019).
Kafri, T. et al. Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line. Genes Dev. 6, 705–714 (1992).
Monk, M., Boubelik, M. & Lehnert, S. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 99, 371–382 (1987).
Seisenberger, S. et al. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol. Cell 48, 849–862 (2012).
Bourc’his, D. & Bestor, T. H. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431, 96–99 (2004).
Ozata, D. M., Gainetdinov, I., Zoch, A., O’Carroll, D. & Zamore, P. D. PIWI-interacting RNAs: small RNAs with big functions. Nat. Rev. Genet. 20, 89–108 (2019).
Aravin, A. A. et al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell 31, 785–799 (2008).
Molaro, A. et al. Two waves of de novo methylation during mouse germ cell development. Genes Dev. 28, 1544–1549 (2014).
Barau, J. et al. The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science 354, 909–912 (2016).
Jain, D. et al. rahu Is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline. PLoS Genet. 13, e1006964 (2017).
Zoch, A. et al. SPOCD1 is an essential executor of piRNA-directed de novo DNA methylation. Nature 584, 635–639 (2020).
Zoch, A. et al. C19ORF84 connects piRNA and DNA methylation machineries to defend the mammalian germ line. Mol. Cell https://doi.org/10.1016/j.molcel.2024.01.014 (2024).
Yoshioka, H., McCarrey, J. R. & Yamazaki, Y. Dynamic nuclear organization of constitutive heterochromatin during fetal male germ cell development in mice. Biol. Reprod. 80, 804–812 (2009).
Santos-Rosa, H. et al. Active genes are tri-methylated at K4 of histone H3. Nature 419, 407–411 (2002).
Vasiliauskaite, L. et al. A MILI-independent piRNA biogenesis pathway empowers partial germline reprogramming. Nat. Struct. Mol. Biol. 24, 604–606 (2017).
Cordes, V. C., Hase, M. E. & Muller, L. Molecular segments of protein Tpr that confer nuclear targeting and association with the nuclear pore complex. Exp. Cell Res. 245, 43–56 (1998).
Cordes, V. C., Reidenbach, S., Rackwitz, H. R. & Franke, W. W. Identification of protein p270/Tpr as a constitutive component of the nuclear pore complex-attached intranuclear filaments. J. Cell Biol. 136, 515–529 (1997).
Mitchell, P. J. & Cooper, C. S. The human tpr gene encodes a protein of 2094 amino acids that has extensive coiled-coil regions and an acidic C-terminal domain. Oncogene 7, 2329–2333 (1992).
Singh, D. et al. The molecular architecture of the nuclear basket. Cell 187, 5267–5281.e13 (2024).
Nakano, H., Funasaka, T., Hashizume, C. & Wong, R. W. Nucleoporin translocated promoter region (Tpr) associates with dynein complex, preventing chromosome lagging formation during mitosis. J. Biol. Chem. 285, 10841–10849 (2010).
Bartlett, B. M. et al. TPR is required for cytoplasmic chromatin fragment formation during senescence. eLife https://doi.org/10.7554/eLife.101702 (2024).
Coyle, J. H., Bor, Y. C., Rekosh, D. & Hammarskjold, M. L. The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway. RNA 17, 1344–1356 (2011).
Pastor, W. A. et al. MORC1 represses transposable elements in the mouse male germline. Nat. Commun. 5, 5795 (2014).
Vasiliauskaite, L. et al. Defective germline reprogramming rewires the spermatogonial transcriptome. Nat. Struct. Mol. Biol. 25, 394–404 (2018).
Watanabe, T. et al. Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. Science 332, 848–852 (2011).
Di Giacomo, M. et al. Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis. Mol. Cell 50, 601–608 (2013).
Carrieri, C. et al. A transit-amplifying population underpins the efficient regenerative capacity of the testis. J. Exp. Med. 214, 1631–1641 (2017).
Wang, H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 910–918 (2013).
Di Giacomo, M., Comazzetto, S., Sampath, S. C., Sampath, S. C. & O’Carroll, D. G9a co-suppresses LINE1 elements in spermatogonia. Epigenetics Chromatin 7, 24 (2014).
Pandey, R. R. et al. Tudor domain containing 12 (TDRD12) is essential for secondary PIWI interacting RNA biogenesis in mice. Proc. Natl Acad. Sci. USA 110, 16492–16497 (2013).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Stringer, C. & Pachitariu, M. Cellpose3: one-click image restoration for improved cellular segmentation. Nat. Methods 22, 592–599 (2025).
Kelly, D. & Chowdhury, T. COIL-Edinburgh/ROI_NucleusColocalisation: nucleus colocalisation v2.01 (2.01). Zenodo https://doi.org/10.5281/zenodo.17200734 (2025).
Schopp, T. et al. The DUF3715 domain has a conserved role in RNA-directed transposon silencing. RNA 29, 1471–1480 (2023).
Rappsilber, J., Ishihama, Y. & Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663–670 (2003).
Chambers, M. C. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918–920 (2012).
Mendes, M. L. et al. An integrated workflow for crosslinking mass spectrometry. Mol. Syst. Biol. 15, e8994 (2019).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).
Jurrus, E. et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 27, 112–128 (2018).
Yariv, B. et al. Using evolutionary data to make sense of macromolecules with a “face-lifted” ConSurf. Protein Sci. 32, e4582 (2023).
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M. & Barton, G. J. Jalview Version 2 — a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).
UniProt, C. UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Res. 53, D609–D617 (2025).
Bankhead, P. et al. QuPath: open source software for digital pathology image analysis. Sci. Rep. 7, 16878 (2017).
Chowdhury, T. tamchow/spocd1_pirna-directed-dna-met-variance: Version of record for manuscript submission (1.0). Zenodo https://doi.org/10.5281/zenodo.17162836 (2025).
Berrens, R. rberrens/SPOCD1-piRNA_directed_DNA_met: 20240114_release (v1.0.2). Zenodo https://doi.org/10.5281/zenodo.10509247 (2024).
Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016).

